QUAL2Kw

theory and documentation

(version 5.1)

QUAL2K

July 16, 2004

A modeling framework for

simulating river and
stream water quality
July 2008
Publication No. 08-03-xxx
printed on recycled paper

This report is available on the Department of Ecology home page on the World Wide Web
at http://www.ecy.wa.gov/biblio/04030??.html
For a printed copy of this report, contact:
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QUAL2K

July 16, 2004

QUAL2Kw
theory and documentation
(version 5.1)
A modeling framework for simulating
river and stream water quality
by
Greg Pelletier and Steve Chapra2
1

Environmental Assessment Program

Olympia, Washington 98504-7710
1
2

Environmental Engineer, Washington State Department of Ecology, Olympia, WA.

Professor and Louis Berger Chair in Computing and Engineering, Tufts University, Medford, MA.

July 2008

Publication No. 08-03-xxx

printed on recycled paper

QUAL2K

July 16, 2004

INTRODUCTION
QUAL2Kw (or Q2K) is a river and stream water quality model that is intended to
represent a modernized version of the QUAL2E (or Q2E) model (Brown and Barnwell
1987). QUAL2Kw is adapted from the QUAL2K model that was originally developed by
Dr. Steven C. Chapra of Tufts University (Chapra and Pelletier, 2003). Q2K is similar to
Q2E in the following respects:

One dimensional. The channel is well-mixed vertically and laterally.

Steady state hydraulics. Non-uniform, steady flow is simulated.
Diel heat budget. The heat budget and temperature are simulated as a function of
meteorology on a diel time scale.
Diel water-quality kinetics. All water quality variables are simulated on a diel
time scale.
Heat and mass inputs. Point and non-point loads and abstractions are simulated.
The QUAL2Kw framework includes the following new elements:

Software Environment and Interface. Q2K is implemented within the Microsoft

Windows environment. It is programmed in the Windows macro language: Visual
Basic for Applications (VBA). Excel is used as the graphical user interface.
Model segmentation. Q2E segments the system into river reaches comprised of
equally spaced elements. In contrast, Q2K uses unequally-spaced reaches. In addition,
multiple loadings and abstractions can be input to any reach.
Carbonaceous BOD speciation. Q2K uses two forms of carbonaceous BOD to
represent organic carbon. These forms are a slowly oxidizing form (slow CBOD) and
a rapidly oxidizing form (fast CBOD).
Anoxia. Q2K accommodates anoxia by reducing oxidation reactions to zero at
low oxygen levels. In addition, denitrification is modeled as a first-order reaction that
becomes pronounced at low oxygen concentrations.
Sediment-water interactions. Sediment-water fluxes of dissolved oxygen and
nutrients are simulated internally rather than being prescribed. That is, oxygen (SOD)
and nutrient fluxes are simulated as a function of settling particulate organic matter,
reactions within the sediments, and the concentrations of soluble forms in the
overlying waters.
Bottom algae. The model explicitly simulates attached bottom algae. These algae
have variable stoichiometry.
Light extinction. Light extinction is calculated as a function of algae, detritus and
inorganic solids.
pH. Both alkalinity and total inorganic carbon are simulated. The rivers pH is
then simulated based on these two quantities.
Pathogens. A generic pathogen is simulated. Pathogen removal is determined as a
function of temperature, light, and settling.

Hyporheic metabolism. Hyporheic exchange and sediment pore water quality are
simulated, including optional simulation of the metabolism of heterotrophic bacteria
in the hyporheic zone.
Automatic calibration. A genetic algorithm is included to determine the optimum
values for the kinetic rate parameters to maximize the goodness of fit of the model
compared with measured data.

The QUAL2K framework does not include the following elements that are included
in Q2E:

Branching. Q2K presently simulates the main stem of a river. It does not model
branches.
Q2K does not presently include an uncertainty component.

QUAL2K

July 16, 2004

GETTING STARTED
Installation is required for many water-quality models. This is not the case for
QUAL2Kw because the model is packaged as an Excel Workbook. The program is
written in Excels macro language: Visual Basic for Applications or VBA. An optional
Fortran executable version of the model is also available to run. The Excel Workbooks
worksheets and charts are used to enter data and display results. Consequently, you
merely have to open the Workbook to begin modeling. The following are the
recommended step-by-step instructions on how to obtain your first model run.
Step 1: Unzip the model files to any folder on the hard drive on your PC. When you
extract the zip archive to a drive or folder on your hard drive, a new subfolder in that
drive or folder will be created with the files for QUAL2Kw. For example, if you
unzipped to your C:\ drive, then a subfolder named C:\qual2kw will be created if it does
not exist, and the QUAL2Kw files will be in a subfolder of the qual2kw folder. The
qual2kw5.xls and qual2kw5.exe files may be copied to any working folder on any drive
of your computer. Both files must be present together in the same working folder for the
Fortran executable to run. Copies of .xls file may be given any name. The qual2kw5.exe
may not be re-named if you want to run the Fortran executable version from the .xls file.
Step 2: Open Excel and make sure that your macro security level is set to medium or low
(Figure 1). This can be done using the menu commands: Tools Macro Security.
Make certain that either the Medium or Low radio button is selected.

Figure 1 The Excel Macro Security Level dialogue box. In order to run Q2K, the Medium
level of security should be selected.

Step 3: Open qual2kw5.xls. When you do this, the Macro Security Dialogue Box will be
displayed if you selected medium security in step 3 (Figure 2).

Figure 2 The Excel Macro security dialogue box. In order to run Q2K, the Enable Macros
button must be selected.

Click on the Enable Macros button.

Figure 3 The QUAL2K Worksheet.

QUAL2K

July 16, 2004

Step 4: Click on either the Run VBA or Run Fortran button (Figure 3). QUAL2K
will begin to execute. Both of these yield identical results except that the Fortran
version runs much faster because it is a compiled executable program. You can follow
the progress of the execution on the status bar that is shown in the bottom left corner
of the worksheet (Figure 4). If the Fortran version is run then a DOS window will
open to show the progress during the integration.

Figure 4 The QUAL2K Status Bar is positioned at the lower left corner of the worksheet. It
allows you to follow the progress of a model run.

If the program runs properly, the Travel Time plot will be displayed. If it does not
work properly, three possibilities exist:
First, you may be using an old version of Microsoft Office. Although Excel is
downwardly compatible for some earlier versions, Q2K will not work with very old
versions.
Second, your computer may not have enough RAM to run the model. The amount of
RAM needed depends on the model application (e.g. number of reaches, calculation time
step, etc.). A minimum RAM of 256 Mb for Windows 98, or 512 Mb with Windows XP is
recommended for small applications, and more is probably needed for larger applications.
Third, you may have made a mistake in implementing the preceding steps. A common
mistake is to make a copy the .xls file in a working folder and forget to also copy the
qual2kw5.exe file to the same working folder (the Fortran executable will not run unless
it is the same working folder as the .xls file)
Occasionally the model may crash. In some cases the crash may result in a Microsoft
Visual Basic error message as shown in Figure 5. If this occurs, click on the End button.
This will terminate the run and bring you back to the Excel Workbook where you can
check for bad input values. If you are proficient in VBA then you may click on the
Debug button to attempt to find out where the program crashed and diagnose the
problem.

10

Figure 5 An example VBA error message that can occur in QUALK2.

Step 5: On the QUAL2K Worksheet click on the Open Old File button. Browse to get to
the working directory. You should see that a new file has been created with the name that
was specified in B9. Click on the Cancel button to return to Q2K.
Note that every time that Q2K is run, a data file will be created with the file name
specified in cell B9 on the QUAL2K Worksheet (Figure 3). The program automatically
affixes the extension .q2k to the file name. Since this will overwrite the file, make certain
to change the file name when you perform a new application. A .q2k file may be opened
by clicking on the Open File button on the QUAL2K Worksheet. This feature allows
you the option to save the inputs for many different simulations without having to save
the .xls for every model run.

QUAL2K

11

July 16, 2004

SEGMENTATION AND HYDRAULICS

The model presently simulates the main stem of a river as depicted in Figure 6.
Tributaries are not modeled explicitly, but can be represented as point sources.
Headwater boundary
1
Point source

Point abstraction

Point abstraction

3
4
5
6

Point source

Non-point
source

Non-point
abstraction

7
Point source

Downstream boundary

Figure 6 QUAL2K segmentation scheme.

Flow Balance
A steady-state flow balance is implemented for each model reach (Figure 7)
Qi Qi 1 Qin ,i Qab ,i

(1)

where Qi = outflow from reach i into the downstream reach i + 1 [m3/d], Qi1 = inflow
from the upstream reach i 1 [m3/d], Qin,i is the total inflow into the reach from point and
nonpoint sources [m3/d], and Qab,i is the total outflow from the reach due to point and
nonpoint abstractions [m3/d].

Qin,i

i1

Qi1

Qab,i

Qi

i+1

12

Figure 7 Reach flow balance.

The total inflow from sources is computed as

Qin,i

psi

npsi

j 1

j 1

Q ps,i, j Qnps,i, j

(2)

where Qps,i,j is the jth point source inflow to reach i [m3/d], psi = the total number of point
sources to reach i, Qnps,i,j is the jth non-point source inflow to reach i [m3/d], and npsi =
the total number of non-point source inflows to reach i.
The total outflow from abstractions is computed as
Qab,i

pai

j 1

Q pa,i , j

npai

Qnpa,i, j

(3)

j 1

where Qpa,i,j is the jth point abstraction outflow from reach i [m3/d], pai = the total number
of point abstractions from reach i, Qnpa,i,j is the jth non-point abstraction outflow from
reach i [m3/d], and npai = the total number of non-point abstraction flows from reach i.
The non-point sources and abstractions are modeled as line sources. As in Figure 8,
the non-point source or abstraction is demarcated by its starting and ending kilometer
points. Its flow is distributed to or from each reach in a length-weighted fashion.
Qnpt

25%Qnpt 25%Qnpt

start

50%Qnpt

end

Figure 8 The manner in which non-point source flow is distributed to a reach.

Hydraulic Characteristics

QUAL2K

13

July 16, 2004

Once the outflow for each reach is computed, the depth and velocity are calculated in one
of three ways: weirs, rating curves, and Manning equations. The program decides among
these options in the following manner:

If a weir height is entered, the weir option is implemented.

If the weir height is zero and a roughness coefficient is entered (n), the Manning
equation option is implemented.
If neither of the previous conditions are met, Q2K uses rating curves.

Weirs
Figure 9 shows how weirs are represented in Q2K. The symbols are defined as: Hi = the
depth of the reach upstream of the weir [m], Hi+1 = the depth of the reach downstream of
the weir [m], elev2i = the elevation above sea level of the tail end of the upstream reach
[m], elev1i+1 = the elevation above sea level of the head end of the downstream reach [m],
Hw = the height of the weir above elev2i [m], Hd = the drop between the elevation above
sea level of the surface of reach i and reach i+1 [m], Hh = the head above the weir [m], Bi
= the width of reach i [m].
(a) Side

(b) Cross-section

Bi
Hi

Hd
Hw

Hh
Hi

Hw

Hi+1
elev2i
elev1i+1

elev2i
elev1i+1

Figure 9 A sharp-crested weir.

For a sharp-crested weir where Hh/Hw < 0.4, flow is related to head by (Finnemore
and Franzini 2002)
Qi 1.83Bi H h3 / 2

(4)

where Qi is the outflow from the segment upstream of the weir in m3/s, and Bi and Hh are
in m. Equation (4) can be solved for
Qi
1.83Bi

H h

2/3

(5)

14

This result can then be used to compute the depth of reach i,

Hi Hw Hh

(6)

and the drop over the weir

H d elev 2 i H i elev1i 1 H i 1

(7)

The velocity and cross-sectional area of reach i can then be computed as

Ac ,i Bi H i

Ui

(8)

Qi
Ac ,i

(9)

Rating Curves
Power equations can be used to relate mean velocity and depth to flow,
U aQ b

(10)

H Q

(11)

where a, b, and are empirical coefficients that are determined from velocity-discharge
and stage-discharge rating curves, respectively. The values of velocity and depth can then
be employed to determine the cross-sectional area and width by
Ac

Q
U

(12)

Ac
H

(13)

The exponents b and typically take on values listed in Table 1. Note that the sum of
b and must be less than or equal to 1. If their sum equals 1, the channel is rectangular.
Table 1 Typical values for the exponents of rating curves used to determine velocity and
depth from flow (Barnwell et al. 1989).

Equation

QUAL2K

Exponent

Typical

15

Range

July 16, 2004

U aQ b

value
0.43

H Q

0.45

0.40.6
0.30.5

Manning Equation
Each reach is idealized as a trapezoidal channel (Figure 10). Under conditions of steady
flow, the Manning equation can be used to express the relationship between flow and
depth as

S 01 / 2 Ac5 / 3
n P2/3

(14)

where Q = flow [m3/s]3, S0 = bottom slope [m/m], n = the Manning roughness coefficient,
Ac = the cross-sectional area [m2], and P = the wetted perimeter [m].

S0
1

H
ss2

ss1

B0

Q, U

Figure 10 Trapezoidal channel.

The cross-sectional area of a trapezoidal channel is computed as

Ac B0 0.5( s s1 s s 2 ) H H

(15)

where B0 = bottom width [m], ss1 and ss2 = the two side slopes as shown in Figure 10
[m/m], and H = reach depth [m].
The wetted perimeter is computed as
P B0 H s s21 1 H s s22 1

(16)

Notice that time is measured in seconds in this and other formulas used to characterize hydraulics. This is
how the computations are implemented within Q2K. However, once the hydraulic characteristics are
determined they are converted to day units to be compatible with other computations.

16

After substituting Eqs. (15) and (16), Eq. (14) can be solved iteratively for depth
(Chapra and Canale 2002),
(Qn) 3 / 5 B0 H k 1 s s21 1 H k 1 s s22 1

Hk
S 3 / 10 B0 0.5( s s1 s s 2 ) H k 1

2/5

(17)

where k = 1, 2, , n, where n = the number of iterations. An initial guess of H0 = 0 is

employed. The method is terminated when the estimated error falls below a specified
value of 0.001%. The estimated error is calculated as
a

H k 1 H k
100%
H k 1

(18)

The cross-sectional area can be determined with Eq. (15) and the velocity can then be
determined from the continuity equation,
U

Q
Ac

(19)

The average reach width, B [m], can be computed as

B

Ac
H

(20)

Suggested values for the Manning coefficient are listed in Table 2.

Table 2 The Manning roughness coefficient for various open channel surfaces (from Chow
et al. 1988).
MATERIAL
Man-made channels
Concrete
Gravel bottom with sides:
concrete
mortared stone
riprap
Natural stream channels
Clean, straight
Clean, winding and some weeds
Weeds and pools, winding
Mountain streams with boulders
Heavy brush, timber

n
0.012
0.020
0.023
0.033
0.025-0.04
0.03-0.05
0.05
0.04-0.10
0.05-0.20

Mannings n typically varies with flow and depth (Gordon et al. 1992). As the depth
decreases at low flow, the relative roughness increases. Typical published values of
Mannings n, which range from about 0.015 for smooth channels to about 0.15 for rough
natural channels, are representative of conditions when the flow is at the bankfull
QUAL2K

17

July 16, 2004

capacity (Rosgen, 1996). Critical conditions of depth for evaluating water quality are
generally much less than bankfull depth, and the relative roughness may be much higher.

Waterfalls
In Section , the drop of water over a weir was computed. This value is needed in order to
compute the enhanced reaeration that occurs in such cases. In addition to weirs, such
drops can also occur at waterfalls (Figure 11).

Hi

Hd

elev2i

Hi+1
elev1i+1

Figure 11 Waterfall.

QUAL2K computes such drops for cases where the elevation above sea level drops
abruptly at the boundary between two reaches. For both the rating curve and the Manning
equation options, the model uses Eq. (7) for this purpose. It should be noted that the drop
is only calculated when the elevation above sea level at the downstream end of a reach is
greater than at the beginning of the next downstream reach; that is, elev2i > elev1i+1.

Travel Time
The residence time of each reach is computed as
k

Vk
Qk

(21)

where k = the residence time of the kth reach [d], Vk = the volume of the kth reach [m3] =
Ac,kxk, and xk = the length of the kth reach [m]. These times are then accumulated to
determine the travel time from the headwater to the downstream end of reach i,
i

t t ,i k
k 1

(22)

where tt,i = the travel time [d].

18

Longitudinal Dispersion
Two options are used to determine the longitudinal dispersion for a boundary between
two reaches. First, the user can simply enter estimated values on the Reach
Worksheet. If the user does not enter values, a formula is employed to internally
compute dispersion based on the channels hydraulics (Fischer et al. 1979),
E p ,i 0.011

U i2 Bi2

(23)

H iU i*

where Ep,i = the longitudinal dispersion between reaches i and i + 1 [m2/s], Ui = velocity
[m/s], Bi = width [m], Hi = mean depth [m], and Ui* = shear velocity [m/s], which is
related to more fundamental characteristics by
U i*

(24)

gH i S i

where g = acceleration due to gravity [= 9.81 m/s 2] and S = channel slope

[dimensionless].
After computing or prescribing Ep,i, the numerical dispersion is computed as
E n ,i

U i xi
2

(25)

The model dispersion Ei (i.e., the value used in the model calculations) is then computed
as follows:

If En,i Ep,i, the model dispersion, Ei is set to Ep,i En,i.

If En,i > Ep,i, the model dispersion is set to zero.

For the latter case, the resulting dispersion will be greater than the physical dispersion.
Thus, dispersive mixing will be higher than reality. It should be noted that for most
steady-state rivers, the impact of this overestimation on concentration gradients will be
negligible. If the discrepancy is significant, the only alternative is to make reach lengths
smaller so that the numerical dispersion becomes smaller than the physical dispersion.

QUAL2K

19

July 16, 2004

TEMPERATURE MODEL
As in Figure 12, the heat balance takes into account heat transfers from adjacent reaches,
loads, abstractions, the atmosphere, and the sediments. A heat balance can be written for
reach i as

Qab,i
dTi Qi 1
Q
E'
E'

Ti 1 i Ti
Ti i 1 Ti 1 Ti i Ti 1 Ti
dt
Vi
Vi
Vi
Vi
Vi
J h ,i
m3

w C pwVi 10 6 cm 3 w C pw H i
W h ,i

J s ,i
m

100 cm w C pw H i

100 cm

(26)

where Ti = temperature in reach i [oC], t = time [d], Ei = the bulk dispersion coefficient
between reaches i and i + 1 [m3/d], Wh,i = the net heat load from point and non-point
sources into reach i [cal/d], w = the density of water [g/cm3], Cpw = the specific heat of
water [cal/(g oC)], Jh,i = the air-water heat flux [cal/(cm2 d)], and Js,i = the sediment-water
heat flux [cal/(cm2 d)].

heat load

inflow
dispersion

atmospheric
transfer

heat abstraction

outflow

dispersion
sediment-water
transfer

sediment

Figure 12 Heat balance.

The bulk dispersion coefficient is computed as

E i'

E i Ac ,i

xi xi 1 / 2

(27)

Note that two types of boundary condition are used at the rivers downstream terminus:
(1) a zero dispersion condition (natural boundary condition) and (2) a prescribed

20

downstream boundary condition (Dirichlet boundary condition). The choice between

these options is made on the Headwater Worksheet.
The net heat load from sources is computed as

psi

j 1

Wh ,i C p

Q ps ,i , j T psi , j

npsi

j 1

Qnps,i, j Tnpsi, j

(28)

where Tps,i,j is the jth point source temperature for reach i [oC], and Tnps,i,j is the jth nonpoint source temperature for reach i [oC].

Surface Heat Flux

As depicted in Figure 13, surface heat exchange is modeled as a combination of five
processes:
J h I (0) J an J br J c J e
(29)

where I(0) = net solar shortwave radiation at the water surface, Jan = net atmospheric
longwave radiation, Jbr = longwave back radiation from the water, Jc = conduction, and
Je = evaporation. All fluxes are expressed as cal/cm2/d.
non-radiation terms

radiation terms

air-water
interface
solar
shortwave
radiation

atmospheric
longwave
radiation

net absorbed radiation

water
longwave
radiation

conduction
and
convection

evaporation
and
condensation

water-dependent terms

Figure 13 The components of surface heat exchange.

Solar Radiation
The model computes the amount of solar radiation entering the water at a particular
latitude (Lat) and longitude (Llm) on the earths surface. This quantity is a function of the

QUAL2K

21

July 16, 2004

radiation at the top of the earths atmosphere which is attenuated by atmospheric

transmission, cloud cover, reflection, and shade,

I ( 0)

I0

at

ac

(1 R s )

extraterrestrial atmospheric cloud

reflection
radiation attenuation attenuation

(30)

(1 S f )
shading

where I(0) = solar radiation at the water surface [cal/cm2/d], I0 = extraterrestrial radiation
(i.e., at the top of the earths atmosphere) [cal/cm2/d], at = atmospheric attenuation, ac =
cloud attenuation, Rs = albedo (fraction reflected), and Sf = effective shade (fraction
blocked by vegetation and topography).
Extraterrestrial radiation. The extraterrestrial radiation is computed as (TVA 1972)
I0

W0
r2

sin

(31)

where W0 = the solar constant [1367 W/m2 or 2823 cal/cm2/d], r = normalized radius of
the earths orbit (i.e., the ratio of actual earth-sun distance to mean earth-sun distance),
and = the suns altitude [radians], which can be computed as
sin sin sin Lat cos cos Lat cos
(32)

where = solar declination [radians], Lat = local latitude [radians], and = the local hour
angle of the sun [radians].
The normalized radius can be estimated as
2

(186 Dy )
365

r 1 0.017 cos
(33)

where Dy = Julian day (Jan. 1 = 1, Jan. 2 = 2, etc.).

The solar declination can be estimated as

22

 23.45

cos
(172 Dy )
180
365

(34)

The local hour angle in radians is given by

trueSolarTime

180
4

180

(35)

where:
trueSolarTime localTime eqtime 4 Llm 60 timezone
(36)

where trueSolarTime is the solar time determined from the actual position of the sun in
the sky [minutes], localTime is the local time in minutes (local standard time), Llm is the
local longitude (positive decimal degrees for the western hemisphere), and timezone is
the local time zone in hours relative to Greenwich Mean Time (e.g. 8 hours for Pacific
Standard Time; the local time zone is selected on the QUAL2K Worksheet). The value
of eqtime represents the difference between true solar time and mean solar time in
minutes of time.
QUAL2K calculates the suns altitude and eqtime, as well as the times of sunrise and
sunset using the Meeus (1999) algorithms as implemented by NOAAs Surface Radiation
Research Branch (www.srrb.noaa.gov/highlights/sunrise/azel.html). The NOAA method
for solar position that is used in QUAL2K also includes a correction for the effect of
atmospheric refraction.
The photoperiod f [hours] is computed as
f t ss t sr
(37)

where tss = time of sunset [hours] and tsr = time of sunrise [hours].
Atmospheric attenuation. Various methods have been published to estimate the fraction
of the atmospheric attenuation from a clear sky (at). Two alternative methods are
available in QUAL2K to estimate at:

Bras (1990)

QUAL2K

23

July 16, 2004

Ryan and Stolzenbach (1972)

Note that the solar radiation model is selected on the Light and Heat Worksheet of
QUAL2K.
The Bras (1990) method computes at as:
at e

n fac a1m

(38)

where nfac is an atmospheric turbidity factor that varies from approximately 2 for clear
skies to 4 or 5 for smoggy urban areas. The molecular scattering coefficient (a1) is
calculated as
a1 0.128 0.054 log10 m
(39)

where m is the optical air mass, calculated as

m

1
sin 0.15( d 3.885) 1.253

(40)

where d is the suns altitude in degrees from the horizon = (180o/).

The Ryan and Stolzenbach (1972) model computes at from ground surface elevation
and solar altitude as:

at atc

288 0.0065 elev

288

5.256

(41)

where atc is the atmospheric transmission coefficient (0.70-0.91, typically approximately

0.8), and elev is the ground surface elevation in meters.
Direct measurements of solar radiation are available at some locations. For example,
NOAAs Integrated Surface Irradiance Study (ISIS) has data from various stations across
the United States (http://www.atdd.noaa.gov/isis.htm). The selection of either the Bras or
Ryan-Stolzenbach solar radiation model and the appropriate atmospheric turbidity factor
or atmospheric transmission coefficient for a particular application should ideally be
guided by a comparison of predicted solar radiation with measured values at a reference
location.
Cloud Attenuation. Attenuation of solar radiation due to cloud cover is computed with

24

a c 1 0.65C L2
(42)

where CL = fraction of the sky covered with clouds.

Reflectivity. Reflectivity is calculated as
Rs A d

(43)

where A and B are coefficients related to cloud cover (Table 3).

Table 3 Coefficients used to calculate reflectivity based on cloud cover.
Cloudiness
CL
Coefficients

Clear
0
A
1.18

B
0.77

Scattered
0.1-0.5
A
B
2.20
0.97

Broken
0.5-0.9
A
0.95

B
0.75

Overcast
1.0
A
B
0.35
0.45

Shade. Shade is an input variable for the QUAL2K model. Shade is defined as the
fraction of potential solar radiation that is blocked by topography and vegetation. An
Excel/VBA program named Shade.xls is available from the Washington Department of
Ecology to estimate shade from topography and riparian vegetation (Ecology 2003).
Input values of integrated hourly estimates of shade for each reach are put into the Shade
Worksheet of QUAL2K.

Atmospheric Long-wave Radiation

The downward flux of longwave radiation from the atmosphere is one of the largest
terms in the surface heat balance. This flux can be calculated using the StefanBoltzmann law
J an Tair 273

sky

1 R L

SKOPi

(44)

where = the Stefan-Boltzmann constant = 11.7x10-8 cal/(cm2 d K4), Tair = air

temperature [oC], sky = effective emissivity of the atmosphere [dimensionless], and RL =
longwave reflection coefficient [dimensionless]. Emissivity is the ratio of the longwave
radiation from an object compared with the radiation from a perfect emitter at the same
temperature. The reflection coefficient is generally small and in typically assumed to
equal 0.03. The term SKOPi is the sky opening fraction (Rutherford et al, 1997).

QUAL2K

25

July 16, 2004

The atmospheric longwave radiation model is selected on the Light and Heat
Worksheet of QUAL2K. Three alternative methods are available for use in QUAL2K to
represent the effective emissivity (sky):
Brutsaert (1982). The Brutsaert equation is physically-based instead of empirically
derived and has been shown to yield satisfactory results over a wide range of atmospheric
conditions of air temperature and humidity at intermediate latitudes for conditions above
freezing (Brutsaert, 1982).
1.333224eair
clear k brut
Ta

1/ 7

where eair is the air vapor pressure [mm Hg], and Ta is the air temperature in K. The
factor of 1.333224 converts the vapor pressure from mm Hg to millibars. Brutsaert
(1982) recommended a default value of 1.24 for kbrut based on typical values for various
physical constants. Several articles have since been published with various recommended
values for kbrut considering the uncertainty and calibration to observations of downwelling
longwave radiation. Crawford and Duchon (1999) suggested a range for kbrut from 1.28 in
January to 1.16 in July with sinusoidal seasonal variaton. Sridhar and Elliot (2002)
recommended an average value for kbrut of 1.31 based on calibration to observed
longwave radiation data in Oklahoma, with values ranging from 1.30 to 1.32 between
four sites. Culf and Gash (1993) also recommended a value of 1.31 instead of 1.24 during
dry seasons in Niger, and a reduced value during wet seasons. QUAL2Kw allows the user
to specify the input value of kbrut and suggests a default value of 1.24.
The air vapor pressure [in mm Hg] is computed as (Raudkivi 1979):
17.27 Td

e air 4.596e

237.3 Td

(45)

where Td = the dew-point temperature [oC].

Brunt (1932). Brunts equation is an empirical model that has been commonly used in
water-quality models (Thomann and Mueller 1987),
clear Aa Ab eair

where Aa and Ab are empirical coefficients. Values of Aa have been reported to range from
about 0.5 to 0.7 and values of Ab have been reported to range from about 0.031 to 0.076
mmHg0.5 for a wide range of atmospheric conditions. QUAL2K uses a default mid-range
value of Aa = 0.6 with Ab = 0.031 mmHg-0.5 if the Brunt method is selected on the Light
and Heat Worksheet.

26

Koberg (1964). Koberg (1964) reported that the Aa in Brunts formula depends on both
air temperature and the ratio of the incident solar radiation to the clear-sky radiation (Rsc).
As in Figure 14, he presented a series of curves indicating that Aa increases with Tair and
decreases with Rsc with Ab held constant at 0.0263 millibars0.5 (about 0.031 mmHg0.5).
The following polynomial is used in Q2K to provide a continuous approximation of
Kobergs curves.
2
Aa a k Tair
bk Tair c k

where
3
2
a k 0.00076437 R sc
0.00121134 R sc
0.00073087 R sc 0.0001106
3
2
bk 0.12796842 R sc
0.2204455 R sc
0.13397992 R sc 0.02586655
3
2
c k 3.25272249 R sc
5.65909609 R sc
3.43402413R sc 1.43052757

The fit of this polynomial to points sampled from Kobergs curves are depicted in Figure
14. Note that an upper limit of 0.735 is prescribed for Aa.

Kobergs A a constant for

Brunts equation for longwave radiation

0.8

Ratio of incident to clear sky radiation Rsc

0.50
0.65
0.75
0.80
0.85

0.7

0.6

0.90
0.95

0.5
1.00
0.4

0.3
-4

12

16

20

24

28

32

Air temperature Tair (oC)

Figure 14 The points are sampled from Kobergs family of curves for determining the
value of the Aa constant in Brunts equation for atmospheric longwave radiation
(Koberg, 1964). The lines are the functional representation used in Q2K.

For cloudy conditions the atmospheric emissivity may increase as a result of

increased water vapor content. High cirrus clouds may have a negligible effect on
atmospheric emissivity, but lower stratus and cumulus clouds may have a significant

QUAL2K

27

July 16, 2004

effect. The Koberg method accounts for the effect of clouds on the emissivity of
longwave radiation in the determination of the Aa coefficient.
Idso (1981). Two equations were proposed by Idso (1981) as summarized by Hatfield et
al. (1983):

Idso 1:
clear 0.179(1.333224eair )1 / 7 exp(350 / Ta )

Idso 2:
clear 0.70 5.95 X 10 5 (1.333224eair ) exp(1500 / Ta )

Idso and Jackson (1969). The following equation was proposed by Idso and Jackson
(1969) (Ta is air temperature in degrees K):
clear 1 0.261exp(0.000777(Ta 273.15) 2 )

Satterlund (1969). The following equation was proposed by Satterlund (1969):

clear 1.08(1 exp((1.333224eair ) (Ta / 2016 ) )

Swinbank (1963). The following equation was proposed by Swinbank (1963):

clear 0.0000092Ta 2
All methods except for Koberg (1964) determine emissivity of a clear sky and do not
account for the effect of clouds. Therefore, the effective atmospheric emissivity for
cloudy skies (sky) is estimated from the clear sky emissivity for all methods except for
Koberg (1964) by using a nonlinear function of the fractional cloud cover (CL) of the
form (TVA, 1972):
sky clear (1 0.17C L2 )
(46)

The selection of the longwave model for a particular application should ideally be
guided by a comparison of predicted results with measured values at a reference location.
However, direct measurements are rarely collected. The Brutsaert method is
recommended to represent a wide range of atmospheric conditions.

28

Water Long-wave Radiation

The back radiation from the water surface is represented by the Stefan-Boltzmann law,
J br T 273

SKOPi

(47)

where = emissivity of water (= 0.97) and T = the water temperature [oC]. The term
SKOPi is the sky opening fraction (Rutherford et al, 1997).

Conduction and Convection

Conduction is the transfer of heat from molecule to molecule when matter of different
temperatures are brought into contact. Convection is heat transfer that occurs due to mass
movement of fluids. Both can occur at the air-water interface and can be described by,

J c c1 f U w Ts Tair
(48)

where c1 = Bowen's coefficient (= 0.47 mmHg/oC). The term, f(Uw), defines the
dependence of the transfer on wind velocity over the water surface where Uw is the wind
speed measured a fixed distance above the water surface.
Many relationships exist to define the wind dependence. Bras (1990), Edinger et al.
(1974), and Shanahan (1984) provide reviews of various methods. Some researchers have
proposed that conduction/convection and evaporation are negligible in the absence of
wind (e.g. Marciano and Harbeck, 1952), which is consistent with the assumption that
only molecular processes contribute to the transfer of mass and heat without wind
(Edinger et al. 1974). Others have shown that significant conduction/convection and
evaporation can occur in the absence of wind (e.g. Brady Graves and Geyer 1969,
Harbeck 1962, Ryan and Harleman 1971, Helfrich et al. 1982, and Adams et al. 1987).
This latter opinion has gained favor (Edinger et al. 1974), especially for waterbodies that
exhibit water temperatures that are greater than the air temperature.
Brady, Graves, and Geyer (1969) pointed out that if the water surface temperature is
warmer than the air temperature, then the air adjacent to the water surface would tend to
become both warmer and more moist than that above it, thereby (due to both of these
factors) becoming less dense. The resulting vertical convective air currents might be
expected to achieve much higher rates of heat and mass transfer from the water surface
[even in the absence of wind] than would be possible by molecular diffusion alone
(Edinger et al. 1974). Water temperatures in natural waterbodies are frequently greater
than the air temperature, especially at night.

QUAL2K

29

July 16, 2004

Edinger et al. (1974) recommend that the relationship that was proposed by Brady,
Graves and Geyer (1969) based on data from cooling ponds, could be representative of
most environmental conditions. Shanahan (1984) recommends that the Lake Hefner
equation (Marciano and Harbeck, 1952) is appropriate for natural waters in which the
water temperature is less than the air temperature. Shanahan also recommends that the
Ryan and Harleman (1971) equation as recalibrated by Helfrich et al. (1982) is best suited
for waterbodies that experience water temperatures that are greater than the air
temperature. Adams et al. (1987) revisited the Ryan and Harleman and Helfrich et al.
models and proposed another recalibration using additional data for waterbodies that
exhibit water temperatures that are greater than the air temperature.
Three options are available on the Light and Heat Worksheet in QUAL2K to
calculate f(Uw):
Brady, Graves, and Geyer (1969)
f (U w ) 19.0 0.95U w2

where Uw = wind speed at a height of 7 m [m/s].

Adams et al. (1987)
Adams et al. (1987) updated the work of Ryan and Harleman (1971) and Helfrich et al.
(1982) to derive an empirical model of the wind speed function for heated waters that
accounts for the enhancement of convection currents when the virtual temperature
difference between the water and air (v in degrees F) is greater than zero. Two wind
functions reported by Adams et al., also known as the East Mesa method, are
implemented in QUAL2K (wind speed in these equations is at a height of 2m).

Adams 1: This formulation uses an empirical function to estimate the effect of

convection currents caused by virtual temperature differences between water and
air, and the Harbeck (1962) equation is used to represent the contribution to
conduction/convection and evaporation that is not due to convection currents
caused by high virtual water temperature.
0.05
2
f (U w ) 0.271 ( 22.4 v1 / 3 ) 2 ( 24.2 Aacres
,iU w, mph )

where Uw,mph is wind speed in mph and Aacres,i is surface area of reach i in acres.
The constant 0.271 converts the original units of BTU ft2 day1 mmHg1 to cal
cm2 day1 mmHg1.

Adams 2: This formulation uses an empirical function of virtual temperature

differences with the Marciano and Harbeck (1952) equation for the contribution to
conduction/convection and evaporation that is not due to the high virtual water
temperature

30

f (U w ) 0.271 ( 22.4 v1 / 3 ) 2 (17U w,mph ) 2

Virtual temperature is defined as the temperature of dry air that has the same density
as air under the in situ conditions of humidity. The virtual temperature difference between
the water and air ( v in F) accounts for the buoyancy of the moist air above a heated
water surface. The virtual temperature difference is estimated from water temperature
(Tw,f in F), air temperature (Tair,f in F), vapor pressure of water and air (es and eair in
mmHg), and the atmospheric pressure (patm is estimated as standard atmospheric pressure
of 760 mmHg in QUAL2K):
Tw, f 460
Tair , f 460

v
460
460
1 0.378e s / p atm
1 0.378e air / p atm

(49)

The height of wind speed measurements is also an important consideration for

estimating conduction/convection and evaporation. QUAL2K internally adjusts the wind
speed to the correct height for the wind function that is selected on the Light and Heat
Worksheet. The input values for wind speed on the Wind Speed Worksheet in
QUAL2K are assumed to be representative of conditions at a height of 7 meters above
the water surface. To convert wind speed measurements (Uw,z in m/s) taken at any height
(zw in meters) to the equivalent conditions at a height of z = 7 m for input to the Wind
Speed Worksheet of QUAL2K, the exponential wind law equation may be used (TVA,
1972):
z
z
w

0.15

U w U wz

(50)

For example, if wind speed data were collected from a height of 2 m, then the wind
speed at 7 m for input to the Wind Speed Worksheet of QUAL2K would be estimated
by multiplying the measured wind speed by a factor of 1.2.

Evaporation and Condensation

The heat loss due to evaporation can be represented by Daltons law,
J e f (U w )(e s e air )
(51)

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31

July 16, 2004

where es = the saturation vapor pressure at the water surface [mmHg], and eair = the air
vapor pressure [mmHg]. The saturation vapor pressure is computed as
17.27T

eair 4.596e 237.3T

(52)

Sediment-Water Heat Transfer

A heat balance for bottom sediment underlying a water reach i can be written as
dT2 ,i
dt

J s ,i J hyp ,i

s C ps H 2,i

(53)

where T2,i = the temperature of the bottom sediment below reach i [oC], Js,i = the
sediment-water conduction heat flux [cal/(cm2 d)], Jhyp,i is the heat flux between the water
and sediment due to hyporheic flow exchange, s = the density of the sediments [g/cm3],
Cps = the specific heat of the sediments [cal/(g oC)], and H2,i = the effective thickness of
the sediment layer [cm]. The quantity s C ps may be estimated as s /s, where s is
the thermal conductivity [cal/(s cm C)] and s is the thermal diffusivity [cm2/s]. The
values of H2,i, s , and s are inputs to the Reach sheet of QUAL2Kw.
The conduction heat flux from the sediments to the water can be computed as

J s ,i

86400 s
T2,i T1,i
H 2 ,i / 2

(54)

where the thermal conductivity s = s s C ps and the constant of 86400 converts units
of cal/cm2/s to cal/cm2/d.
The thermal properties of some natural sediments along with its components are
summarized in Table 4. Note that soft, gelatinous sediments found in the deposition zones
of lakes are very porous and approach the values for water. Some very slow, impounded
rivers may approach such a state. However, rivers tend to have coarser sediments with
significant fractions of sands, gravels and stones. Upland streams can have bottoms that
are dominated by boulders and rock substrates.
Inspection of the component properties of Table 4 suggests that the presence of solid
material in stream sediments leads to a higher coefficient of thermal diffusivity than that

32

for water or porous lake sediments. In Q2K, we suggest a default value of 0.0064 cm2/s
for this quantity.

QUAL2K

33

July 16, 2004

Table 4 Thermal properties for natural sediments and the materials that comprise natural
sediments.

In addition, specific heat tends to decrease with density. Thus, the product of these
two quantities tends to be more constant than the multiplicands. Nevertheless, it appears
that the presence of solid material in stream sediments leads to a lower product than that
for water or gelatinous lake sediments. In Q2K, we suggest a default value of 1.6 W/(m
C) for the thermal conductivity.
A sediment thickness of 10 cm is recommended in the absence of significant
hyporheic exchange in order to capture the effect of the sediments on the diel heat budget
for the water (Appendix C). If hyporheic flow exchange is significant, then the effective
thickness of the hyporheic zone of rapid transient storage may typically range from about
20 to 300% of the stream depth (Harvey and Wagner, 2000; Gooseff et al., 2003), with
higher relative values in smaller streams. The residence time of materials in the transient
scale hyporheic zone is typically on the order of 0.01 to 10 days (Poole and Berman,
2001).

34

The transient storage zone is the location of exchange of main channel flow with
subsurface hyporheic flow and surface water dead zones. The hyporheic zone is the layer
of saturated sediment that is adjacent to and underneath the stream. The hyporheic zone
is hydraulically connected to the stream, and stream flow continually exchanges in and
out of the hyporheic zone. The hydraulic characteristics such as size and exchange rates
between the water column and the transient storage or hyporheic zone can be estimated
by fitting an advection-dispersion-transient storage zone model similar to that of Bencala
and Walters (1983). An efficient method for estimating the parameters of the hyporheic
zone volume and exchange rate is provided by Hart (1995).
Significant amounts of flow exchange can occur depending on geomorphic controls.
Kasahara and Wondzell (2003) report flow exchange ranging from about 0.6-5% of the
total surface flow per 100 meter in fifth-order streams, up to 76 to >100% of the total
surface flow per 100 meter in second-order streams. Fernald et al. (2001) reported >72%
of the surface flow of the eighth-order Willamette River exchanged with the transient
storage and hyporheic zones with a thickness on the order of 20-30% of the stream depth
and residence times of 0.2-30 hour over a 26 km reach. In general, smaller streams
usually have higher proportions of surface flow in and out of the hyporheic zone
compared with larger streams.
The heat flux from hyporheic exchange of water between the stream and the
hyporheic sediment zone is computed as
J hyp ,i

'
Ehyp
,i C p

Asf ,i

2 ,i

100 cm

T1,i

(55)
'

where E hyp ,i is the bulk hyporheic exchange flow in reach i [m3/day], and Asf,i is the
surface area of the hyporheic zone in reach i (m2). The hyporheic exchange flow is an
input to the Reach sheet of Q2K, and the surface area is computed from reach length and
channel width also based on inputs to the Reach sheet.

QUAL2K

35

July 16, 2004

CONSTITUENT MODEL
Constituents and General Mass Balance
The model constituents are listed in Table 5. The constituents in the water column are
indicated by either the subscript 1 or no subscript, and in the hyporheic pore water zone
are indicated by the subscript 2 except for attached bottom algae in the water column
(ab INb, IPb) and heterotrophic bacteria in the hyporheic sediment zone (ah).
Table 5 Model state variables
Variable
Conductivity
Inorganic suspended solids
Dissolved oxygen
Slow-reacting CBOD
Fast-reacting CBOD
Organic nitrogen
Ammonia nitrogen
Nitrate nitrogen
Organic phosphorus
Inorganic phosphorus
Phytoplankton
Detritus
Pathogen
Generic constituent
Alkalinity
Total inorganic carbon
Bottom algae (ab in the surface water layer), biofilm
of attached heterotrophic bacteria (ah in the
hyporheic sediment zone for the Level 2 option)
Bottom algae nitrogen
Bottom algae phosphorus

Symbol

Units*

s1, s2
mi,1, mi,2
o1, o2
cs,1, cs,2
cf,1, cf,2
no,1, no,2
na,1, na,2
nn,1, nn,2
po,1, po,2
pi,1, pi,2
ap,1, ap,2
mo,1, mo,2
x1, x2
gen1, gen2
Alk1, Alk2
cT,1, cT,2
ab,ah

mhos
mgD/L
mgO2/L
mg O2/L
mg O2/L
gN/L
gN/L
gN/L
gP/L
gP/L
gA/L
mgD/L
cfu/100 mL
user defined
mgCaCO3/L
mole/L
gD/m2

INb
IPb

mgN/m2
mgP/m2

* mg/L g/m3

Simulation of water quality constituents in the hyporheic sediment pore water is

optional in Q2K. Three options are provided:

No hyporheic simulation: mass transfer between the water column and

hyporheic pore water, and water quality kinetics in the hyporheic pore water will
not be simulated.
Level 1: simulation of zero-order or first-order oxidation of fast-reacting CBOD
with attenuation from CBOD and dissolved oxygen in the hyporheic sediment
zone.

Level 2: simulation of heterotrophic bacteria biofilm growth (zero-order or firstorder), respiration, and death with attenuation of growth from CBOD, dissolved
oxygen, ammonia, nitrate, and inorganic phosphorus in the hyporheic pore water
zone.

For all but the bottom algae variables, a general mass balance for a constituent in the
water column of a reach is written as (Figure 15)
'
E hyp
Qab ,i
dci Qi 1
Qi
Ei'1
Ei'
Wi

ci 1 ci
ci
ci 1 ci ci1 ci S i ,i c2,i ci
dt
Vi
Vi
Vi
Vi
Vi
Vi
Vi

(56)

where Wi = the external loading of the constituent to reach i [g/d or mg/d], and Si =
sources and sinks of the constituent due to reactions and mass transfer mechanisms
[g/m3/d or mg/m3/d]. Exchange of mass between the surface water and the hyporheic
'
sediment zone is represented by the bulk hyporheic exchange flow in reach i [ E hyp ,i in
m3/day] and the difference in concentration in the surface water (ci) and in the hyporheic
sediment zone (c2,i).

mass load

atmospheric
transfer

inflow

mass abstraction

outflow

dispersion

bottom algae

dispersion

sediments

Figure 15 Mass balance.

For all but the heterotrophic bacteria biofilm, the general mass balance for a
constituent concentration in the hyporheic sediment zone of a reach (c2,i) is written as
dc 2,i
dt

S 2 ,i

'
E hyp
,i

V 2 ,i

c 2 ,i

(57)

where S2,i = sources and sinks of the constituent in the hyporheic zone due to
reactions, V2,i = s ,i Ast ,i H 2,i / 100 = volume of pore water in the hyporheic sediment
zone [m3], s ,i is the porosity of the hyporheic sediment zone [dimension less number
between 0 and 1], Ast,i = the surface area of the reach [m2], and H2,i = the thickness of the

38

hyporheic zone [cm]. Porosity is defined as the fraction of the total volume of sediment
that is in the liquid phase and is interconnected (Chapra, 1997).
The external load is computed as
psi

npsi

j 1

j 1

Wi Q ps ,i , j c psi , j Qnps ,i , j c npsi , j

(58)

where cps,i,j is the jth point source concentration for reach i [mg/L or g/L], and cnps,i,j is the
jth non-point source concentration for reach i [mg/L or g/L].
For bottom algae, the transport and loading terms are omitted,
dab , i
dt

Sb,i

(59)

dIN b
S bN ,i
dt

(60)

dIPb
S bP ,i
dt

(61)

where Sb,i = sources and sinks of bottom algae biomass due to reactions [gD/m2/d], SbN,i =
sources and sinks of bottom algae nitrogen due to reactions [mgN/m2/d], and SbP,i =
sources and sinks of bottom algae phosphorus due to reactions [mgP/m2/d].
For heterotrophic bacteria in the hyporheic sediment zone (Level 2 option), the
transport and loading terms are omitted,
dah ,i
S ah ,i
dt

(62)

where Sah,i = sources and sinks of heterotrophic bacteria in the hyporheic sediment zone
due to reactions [gD/m2/d].
Settled inorganic suspended solids, phytoplankton, and detritus are assumed to be
deposited from the water column layer to the sediment diagenesis zone and do not enter
the hyporheic pore water. The rationale for this assumption is that hyporheic exchange
typically does not occur in depositional areas of fine sediment. The sediment diagenesis
sub-model accounts for anaerobic metabolism of settled material in the sediment. The
hyporheic sub-model accounts for aerobic metabolism of heterotrophic bacteria in the
hyporheic zone. Suspended materials are transported to the hyporheic pore water for the
Level 1 and Level 2 simulation options of hyporheic metabolism.

QUAL2K

39

July 16, 2004

The sources and sinks for the state variables are depicted in Figure 16 (note that the
internal levels of nitrogen and phosphorus in the bottom algae are not depicted). The
mathematical representation of these processes are presented in the following sections.
re

rda
ds

mo

rod

cs

ox

cT

cf

se

no

na

se

sod

cf

X
s

cT
rna

cT

ox

s
nn

mi

dn

Alk

se

cT

rpa
s

po

IN

pi
s

se

IP

u
e

o
cT

Figure 16 Model kinetics and mass transfer processes. The state variables are defined in
Table 5. Kinetic processes are dissolution (ds), hydrolysis (h), oxidation (ox),
nitrification (n), denitrification (dn), photosynthesis (p), respiration (r), excretion
(e), death (d), respiration/excretion (rx). Mass transfer processes are reaeration
(re), settling (s), sediment oxygen demand (SOD), sediment exchange (se), and
sediment inorganic carbon flux (cf).

Reaction Fundamentals
Biochemical Reactions
The following chemical equations are used to represent the major biochemical
reactions that take place in the model (Stumm and Morgan 1996):
Plant Photosynthesis and Respiration:
Ammonium as substrate:
2
106CO 2 16 NH
108H 2 O
4 HPO 4

P
C106 H 263 O110 N 16 P1 107O 2 14 H

(63)

40

Nitrate as substrate:

106CO 2 16 NO 3
HPO 2
122H 2 O + 18H +
4

P
C106 H 263 O110 N16 P1 138O 2

(64)

Nitrification:
NH 4 2O 2 NO 3 H 2 O 2H

(65)

Denitrification:
5CH 2 O 4NO 3 4H 5CO 2 2N 2 7H 2 O

(66)

Note that a number of additional reactions are used in the model such as those involved
with simulating pH and unionized ammonia. These will be outlined when these topics
are discussed later in this document.

Stoichiometry of Organic Matter

The model requires that the stoichiometry of organic matter (i.e., phytoplankton and
detritus) be specified by the user. The following representation is suggested as a first
approximation (Redfield et al. 1963, Chapra 1997),
100 gD : 40 gC : 7200 mgN :1000 mgP :1000 mgA

(67)

where gX = mass of element X [g] and mgY = mass of element Y [mg]. The terms D, C,
N, P, and A refer to dry weight, carbon, nitrogen, phosphorus, and chlorophyll a,
respectively. It should be noted that chlorophyll a is the most variable of these quantities
with a range of approximately 500-2000 mgA (Laws and Chalup 1990, Chapra 1997).
These values are then combined to determine stoichiometric ratios as in
rxy

gX
gY

(68)

For example, the amount of detritus (in dry weight) that is released due to the death of 1
mgA of phytoplankton can be computed as
rda

100 gD
gD
0.1
1000 mgA
mgA

Oxygen Generation and Consumption

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41

July 16, 2004

The model requires that the rates of oxygen generation and consumption be prescribed. If
ammonia is the substrate, the following ratio (based on Eq. 60) can be used to determine
the grams of oxygen generated for each gram of plant matter that is produced through
photosynthesis.
roca

107 moleO 2 (32 gO 2 /moleO 2 )

gO 2
2.69
106 moleC(12 gC/moleC)
gC

(69)

If nitrate is the substrate, the following ratio (based on Eq. 61) applies
rocn

138 moleO 2 (32 gO 2 /moleO 2 )

gO 2
3.47
106 moleC(12 gC/moleC)
gC

(70)

Note that Eq. (60) is also used for the stoichiometry of the amount of oxygen
consumed for plant respiration.
For nitrification, the following ratio is based on Eq. (62)
ron

2 moleO 2 (32 gO 2 /moleO 2 )

gO 2
4.57
1 moleN(14 gN/moleN)
gN

(71)

CBOD Utilization Due to Denitrification

As represented by Eq. (63), CBOD is utilized during denitrification,
rondn 2.67

gO 2 5 moleC 12 gC/moleC
gO 2
1 gN

0.00286
gC 4 moleN 14 gN/moleN 1000 mgN
mgN

(72)

Temperature Effects on Reactions

The temperature effect for all first-order reactions used in the model is represented by
k (T ) k ( 20) T 20

(73)

where k(T) = the reaction rate [/d] at temperature T [oC] and = the temperature
coefficient for the reaction.

Composite Variables
In addition to the model's state variables, Q2K also displays several composite variables
that are computed as follows:
Total Organic Carbon (mgC/L):
42

TOC

cs c f
roc

rca a p rcd mo

(74)

Total Nitrogen (gN/L):

TN no na nn rna a p

(75)

Total Phosphorus (gP/L):

TP po pi rpa a p

(76)

Total Kjeldahl Nitrogen (gN/L):

TKN no na rna a p

(77)

Total Suspended Solids (mgD/L):

TSS rda a p m o mi

(78)

Ultimate Carbonaceous BOD (mgO2/L):

CBODu c s c f roc rca a p roc rcd mo

(79)

Relationship of Model Variables and Data

For all but slow and fast CBOD (cf and cs), there exists a relatively straightforward
relationship between the model state variables and standard water-quality measurements.
These are outlined next. Then we discuss issues related to the more difficult problem of
measuring CBOD.

Non-CBOD Variables and Data

The following are measurements that are needed for comparison of non-BOD variables
with model output:
TEMP = temperature (oC)
TKN = total kjeldahl nitrogen (gN/L) or TN = total nitrogen (gN/L)
NH4 = ammonium nitrogen (gN/L)
NO2 = nitrite nitrogen (gN/L)
NO3 = nitrate nitrogen (gN/L)
CHLA = chlorophyll a (gA/L)
TP = total phosphorus (gP/L)

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43

July 16, 2004

SRP = soluble reactive phosphorus (gP/L)

TSS = total suspended solids (mgD/L)
VSS = volatile suspended solids (mgD/L)
TOC = total organic carbon (mgC/L)
DOC = dissolved organic carbon (mgC/L)
DO = dissolved oxygen (mgO2/L)
PH = pH
ALK = alkalinity (mgCaCO3/L)
COND = specific conductance (mhos)
The model state variables can then be related to these measurements as follows:
s = COND
mi = TSS VSS or TSS rdc (TOC DOC)
o = DO
no = TKN NH4 rna CHLA

or

no = TN NO2 NO3 NH4 rna CHLA

na = NH4
nn = NO2 + NO3
po = TP SRP rpa CHLA
pi = SRP
ap = CHLA
mo = VSS rda CHLA or rdc (TOC DOC) rda CHLA
pH = PH
Alk = ALK

Carbonaceous BOD
The interpretation of BOD measurements in natural waters is complicated by three
primary factors:

Filtered versus unfiltered. If the sample is unfiltered, the BOD will reflect
oxidation of both dissolved and particulate organic carbon. Since Q2K
distinguishes between dissolved (cs and cf) and particulate (mo and ap) organics, an
unfiltered measurement alone does not provide an adequate basis for
distinguishing these individual forms. In addition, one component of the
44

particulate BOD, phytoplankton (ap) can further complicate the test through
photosynthetic oxygen generation.

Nitrogenous BOD. Along with the oxidation of organic carbon (CBOD),

nitrification also contributes to oxygen depletion (NBOD). Thus, if the sample (a)
contains reduced nitrogen and (b) nitrification is not inhibited, the measurement
includes both types of BOD.

Incubation time. Short-term, usually 5-day, BODs are typically performed.

Because Q2K uses ultimate CBOD, 5-day BODs must be converted to ultimate
BODs in a sensible fashion.

We suggest the following as practical ways to measure CBOD in a manner that

accounts for the above factors and results in measurements that are compatible with Q2K.
Filtration. The sample should be filtered prior to incubation in order to separate
dissolved from particulate organic carbon.
Nitrification inhibition. Nitrification can be suppressed by adding a chemical inhibiting
agent such as TCMP (2-chloro-6-(trichloro methyl) pyridine. The measurement then truly
reflects CBOD. In the event that inhibition is not possible, the measured value can be
corrected for nitrogen by subtracting the oxygen equivalents of the reduced nitrogen (=
ron TKN) in the sample. However, as with all such difference-based adjustments, this
correction may exhibit substantial error.
Incubation time. The model is based on ultimate CBOD, so two approaches are
possible: (1) use a sufficiently long period so that the ultimate value is measured, or (2)
use a 5-day measurement and extrapolate the result to the ultimate. The latter method is
often computed with the formula
CBODFNU

CBODFN5
1 e k1 5

(80)

where CBODFNU4 = the ultimate dissolved carbonaceous BOD [mgO2/L], CBODFN5 =

the 5-day dissolved carbonaceous BOD [mgO2/L], and k1 = the CBOD decomposition
rate in the bottle [/d].
It should be noted that, besides practical considerations of time and expense, there
may be other benefits from using the 5-day measurement with extrapolation, rather that
performing the longer-term CBOD. Although extrapolation does introduce some error,
the 5-day value has the advantage that it would tend to minimize possible nitrification
effects which, even when inhibited, can begin to be exerted on longer time frames.

The nomenclature FNU stands for Filtration, Nitrification inhibition and Ultimate

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45

July 16, 2004

If all the above provisions are implemented, the result should correspond to the model
variables by
cf + cs = CBODFNU
Slow versus Fast CBOD. The final question relates to discrimination between fast and
slow CBODU. Although we believe that there is currently no single, simple,
economically-feasible answer to this problem, we think that the following 2 strategies
represent the best current alternatives.
Option 1: Represent all the dissolved, oxidizable organic carbon with a single pool (fast
CBOD). It will still be necessary to specify rate parameters for slow CBOD because the
process of dissolution of particulate organic carbon in detritus contributes to slow CBOD.
If no slow CBOD inputs are entered for headwater, point sources, or nonpoint sources,
then slow CBOD will most likely exert a very minor influence on dissolved oxygen and it
is effectively dropped from the model. For this case,
cf = CBODFNU
cs = 0
Option 2: Use an ultimate CBOD measurement for the fast fraction and compute slow
CBOD by difference with a DOC measurement. For this case,
cf = CBODFNU
cs = rocDOC CBODFNU
Option 2 works very nicely for systems where two distinct types of CBOD are
present. For example, sewage effluent and autochthonous carbon from the aquatic food
chain might be considered as fast CBOD. In contrast, industrial wastewaters such as pulp
and paper mill effluent or allochthonous DOC from the watershed might be considered
more recalcitrant and hence could be lumped into the slow CBOD fraction. In such case,
the hydrolysis rate converting the slow into the fast fraction could be set to zero to make
the two forms independent, and the cs and cf could each be represented by CBODFNU
data from their respective sources (e.g. for some sources such as municipal wastewaters
the CBODFNU could contribute to cf, and for others such as pulp mill effluents with more
refractory organic carbon their CBODFNU could contribute to cs).
For options 1 and 2, the CBODFNU can either be (a) measured directly using a long
incubation time or (b) computed by extrapolation with Eq. 75. In both situations, a time
frame of several weeks to a month (i.e., a 20- to 30-day CBOD) is probably a valid period
in order to oxidize most of the readily degradable organic carbon. We base this
assumption on the fact that bottle rates for sewage-derived organic carbon are on the
order of 0.05 to 0.3/d (Chapra 1997). As in Figure 17, such rates suggest that much of the
readily oxidizable CBOD will be exerted in about 20 to 30 days.

46

Figure 17 Progression of CBOD test for various levels of the bottle decomposition rate.

In addition, we believe that practitioners should consider conducting long-term

CBOD tests at 30oC rather than at the commonly employed temperature of 20oC. The
choice of 20oC originated from the fact that the average daily temperature of most
receiving waters and wastewater treatment plants in the temperate zone in summer is
approximately 20oC.
If the CBOD measurement is intended to be used for regulation or to assess treatment
plant performance, it makes sense to standardize the test at a particular temperature. And
for such purposes, 20oC is as reasonable a choice as any. However, if the intent is to
measure an ultimate CBOD, anything that speeds up the process while not jeopardizing
the measurement's integrity would seem beneficial.
The saprophytic bacteria that break down nonliving organic carbon in natural waters
and sewage thrive best at temperatures from 20C to 40C. Thus, a temperature of 30oC is
not high enough that the bacterial assemblage would shift to thermophilic organisms that
are atypical of natural waters and sewage. The benefit should be higher oxidation rates
which would result in shorter analysis times for CBOD measurements. Assuming that a
Q10 2 is a valid approximation for bacterial decomposition, a 20-day BOD at 30oC
should be equivalent to a 30-day BOD at 20oC.
In some cases where available data are very limited and only 5-day BOD (BOD5)
data are available to represent organic carbon, it may be reasonable to use a simplification
of option 1 by assuming that BOD5 is approximately equivalent to of CBODFN5. If the
BOD decay rate constant is assumed to be a typical value of about -0.23 day-1 (Brown
and Barnwell, 1985), then the fast CBOD could be approximated as about 1.46 X BOD5.
A better simple alternative could be to estimate the carbonaceous fraction of the total
BOD5 (CBOD5) from literature summaries or available data and then estimate the fast
CBOD as 1.46 X CBOD5.

Constituent Reactions

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47

July 16, 2004

The mathematical relationships that describe the individual reactions and concentrations
of the model state variables (Table 5) are presented in the following paragraphs.

Conservative Substance (s)

By definition, conservative substances are not subject to reactions:
(81)

Ss = 0

Phytoplankton (ap)
Phytoplankton increase due to photosynthesis. They are lost via respiration, death, and
settling
S ap PhytoPhoto PhytoResp PhytoDeath PhytoSettl

(82)

Photosynthesis
Phytoplankton photosynthesis is computed as
PhytoPhoto p a p

(83)

where p = phytoplankton photosynthesis rate [/d] is a function of temperature, nutrients,

and light,
p k gp (T ) Np Lp

(84)

where kgp(T) = the maximum photosynthesis rate at temperature T [/d], Np =

phytoplankton nutrient attenuation factor [dimensionless number between 0 and 1], and
Lp = the phytoplankton light attenuation coefficient [dimensionless number between 0
and 1].
Nutrient Limitation. Michaelis-Menten equations are used to represent growth
limitation for inorganic nitrogen, phosphorus and inorganic carbon. The minimum value
is then used to compute the nutrient attenuation factor,

na nn
pi
[ H 2 CO *3 ] [ HCO 3 ]
,
,
k sNp n a n n k sPp p i k sCp [ H 2 CO *3 ] [ HCO 3 ]

Np min

(85)

where ksNp = nitrogen half-saturation constant [gN/L] ksPp = phosphorus half-saturation

constant [gP/L], ksCp = inorganic carbon half-saturation constant [mole/L], [H2CO3*] =

48

dissolved carbon dioxide concentration [mole/L], and [HCO3] = bicarbonate

concentration [mole/L].
Light Limitation. It is assumed that light attenuation through the water follows the BeerLambert law,
PAR ( z ) PAR (0)e ke z

(86)

where PAR(z) = photosynthetically available radiation (PAR) at depth z below the

water surface [ly/d]5, and ke = the light extinction coefficient [m1]. The PAR at the
water surface is assumed to be a fixed fraction of the solar radiation:
PAR(0) = 0.47 I(0)
The extinction coefficient is related to model variables by
k e k eb i mi o mo p a p pn a 2p / 3 mac ab / H i

(87)

where keb = the background coefficient accounting for extinction due to water and
color [/m], i, o, p, pn,, and mac are constants accounting for the impacts of
inorganic suspended solids [L/mgD/m], particulate organic matter [L/mgD/m], and
chlorophyll [L/gA/m and (L/gA)2/3/m], and macrophytes [m3/gD/m], respectively.
Suggested values for these coefficients are listed in Table 6.
Table 6 Suggested values for light extinction coefficients
Symbol

Value

i
o
p
pn
mac
mac
mac
mac

0.052
0.174
0.0088
0.054
0.01
0.006
0.013 to 0.019
0.024

Reference

Di Toro (1978)
Di Toro (1978)
Riley (1956)
Riley (1956)
Ikusima, 1970 (Myriophyllum spicatum)
Titus and Adams, 1979 (Myriophyllum spicatum)
Titus and Adams, 1979 (Vallisneria americana)
Van der Bijl et al., 1989 (Potamogeton pectinatus)

Three models are used to characterize the impact of light on phytoplankton

photosynthesis (Figure 18):

ly/d = langley per day. A langley is equal to a calorie per square centimeter. Note that a ly/d is related to
the E/m2/d by the following approximation: 1 E/m2/s 0.45 Langley/day (LIC-OR, Lincoln, NE).

QUAL2K

49

July 16, 2004

Smith

Steele
Half-saturation

0.5

0
0

100

200

300

400

500

Figure 18 The three models used for phytoplankton and bottom algae photosynthetic light
dependence. The plot shows growth attenuation versus PAR intensity [ly/d].

Half-Saturation (Michaelis-Menten) Light Model (Baly 1935):

FLp

I ( z)
K Lp I ( z )

(88)

where FLp = phytoplankton growth attenuation due to light and KLp = the
phytoplankton light parameter. In the case of the half-saturation model, the light
parameter is a half-saturation coefficient [ly/d]. This function can be combined with
the Beer-Lambert law and integrated over water depth, H [m], to yield the
phytoplankton light attenuation coefficient
Lp

K Lp I (0)
1
ln
k e H K Lp I (0)e ke H

(89)

Smiths Function (Smith 1936):

FLp

I ( z)
2
K Lp

(90)

I ( z) 2

where KLp = the Smith parameter for phytoplankton [ly/d]; that is, the PAR at which
growth is 70.7% of the maximum. This function can be combined with the Beer-Lambert
law and integrated over water depth to yield
Lp

I (0) / K Lp 1 I (0) / K Lp 2

ln
k e H I (0) / K e ke H 1 I (0) / K e ke H
Lp
Lp

(91)

Steeles Equation (Steele 1962):

50

FLp

I (z)

e
K Lp

I (z)
K Lp

(92)

where KLp = the PAR at which phytoplankton growth is optimal [ly/d]. This function can
be combined with the Beer-Lambert law and integrated over water depth to yield
Lp

I ( 0)
I (0) e ke H

2.718282
K Lp
K Lp

e
e
ke H

(93)

Losses
Respiration. Phytoplankton respiration is represented as a first-order rate that is
attenuated at low oxygen concentration,
PhytoResp Foxp k rp (T ) a p

(94)

where krp(T) = temperature-dependent phytoplankton respiration rate [/d] and Foxp =

attenuation due to low oxygen [dimensionless]. Oxygen attenuation is modeled by Eqs.
(111) to (113) with the oxygen dependency represented by the parameter Ksop.
Death. Phytoplankton death is represented as a first-order rate,
PhytoDeath k dp (T ) a p

(95)

where kdp(T) = temperature-dependent phytoplankton death rate [/d].

Settling. Phytoplankton settling is represented as
PhytoSettl

va
ap
H

(96)

where va = phytoplankton settling velocity [m/d].

Bottom algae (ab)

Bottom algae increase due to photosynthesis. They are lost via respiration and death.
S b BotAlgPhoto BotAlgResp BotAlgDeath

(97)

Photosynthesis

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July 16, 2004

Two representations can be used to model bottom algae photosynthesis is a

simplification. The first is based on a temperature-corrected zero-order rate attenuated by
nutrient and light limitation (Rutherford et al. 1999),
BotAlgPhoto C gb (T ) Nb Lb

(98)

where Cgb(T) = the zero-order temperature-dependent maximum photosynthesis rate [gD/

(m2 d)], Nb = bottom algae nutrient attenuation factor [dimensionless number between 0
and 1], and Lb = the bottom algae light attenuation coefficient [dimensionless number
between 0 and 1].
The second uses a first-order model,
BotAlgPhoto C gb (T ) Nb Lb Sb a b

(99)

where, for this case, Cgb(T) = the first-order temperature-dependent maximum

photosynthesis rate [d1], and Sb = bottom algae space limitation attenuation factor.
Temperature Effect. As for the first-order rates, an Arrhenius model is employed to
quantify the effect of temperature on bottom algae photosynthesis,
C gb (T ) C gb ( 20) T 20

(100)

Nutrient Limitation. The effect of nutrient limitation on bottom plant photosynthesis is

modeled in a different way than for the phytoplankton. Rather than being dependent on
external nutrient concentration, the photosynthesis rate is dependent on intracellular
nutrients using a formulation originally developed by Droop (1974),

Nb

q0 N
q0P
[ H 2 CO *3 ] [HCO 3 ]
min 1
,1
,

qN
q P k sCb [H 2 CO *3 ] [ HCO 3 ]

(101)

where qN and qP = the cell quotas of nitrogen [mgN gD1] and phosphorus [mgP gD1],
respectively, q0N and q0P = the minimum cell quotas of nitrogen [mgN gD1] and
phosphorus [mgP gD1], respectively, and , ksCb = inorganic carbon half-saturation
constant for the bottom algae [mole/L]. The minimum cell quotas are the levels of
intracellular nutrient at which growth ceases.
The cell quotas represent the ratios of the intracellular nutrient to the bottom plants
dry weight,
qN

IN b
ab

(102)

52

qP

IPb
ab

(103)

where INb = intracellular nitrogen concentration [mgN/m2] and IPb = intracellular

phosphorus concentration [mgP/m2].
The change in intracellular nitrogen and phosphorus in bottom algal cells is calculated
from
S bN BotAlgUptakeN q N BotAlgDeath q N k excb (T )ab

(104)

S bP BotAlgUptakeP q P BotAlgDeath q P k excb (T )ab

(105)

where BotAlgUptakeN and BotAlgUptakeP = uptake rates for nitrogen and phosphorus in
bottom algae (mgN/m2/d and mgP/m2/d), kexcb(T) = the temperature-dependent bottom
algae excretion rate [/d], and BotAlgDeath is the death term for bottom algae (gD/m2/d)
as defined in the Losses subsection below. The N and P uptake rates depend on both
external and intracellular nutrients as in (Rhee 1973),
BotAlgUptakeN mN

K qN
na nn
ab
k sNb n a n n K qN (q N q 0 N )

(106)

BotAlgUptakeP mP

K qP
pi
ab
k sPb p i K qP ( q P q 0 P )

(107)

where mN and mP = the maximum uptake rates for nitrogen [mgN/gD/d] and phosphorus
[mgP/gD/d], respectively, ksNb and ksPb = half-saturation constants for external nitrogen
[gN/L] and phosphorus [gP/L], respectively and KqN and KqP = half-saturation
constants for intracellular nitrogen [mgN gD1] and phosphorus [mgP gD1], respectively.
Light Limitation. If bottom plants represent macrophytes, then light limitation is
determined by the PAR in the integrated water column similar to the method for
phytoplankton. Bottom plants are assumed to represent macrophytes if any N or P uptake
is specified to occur from the sediments. If bottom plants represent periphyton or bottom
algae instead of macrophytes, then light limitation at any time is determined by the
amount of PAR reaching the bottom of the water column. The quantity of bottom light is
computed with the Beer-Lambert law (recall Eq. 76) evaluated at the bottom of the river,
I ( H ) I (0)e ke H

(108)

As with the phytoplankton, three models (Eqs. 78, 80 and 82) are used to characterize the
impact of light on bottom algae photosynthesis. Substituting Eq. (98) into these
models yields the following formulas for the bottom algae light attenuation
coefficient,
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53

July 16, 2004

Half-Saturation Light Mode (Baly 1935):

Lb

I (0)e ke H

K Lb I (0)e ke H

(109)

Smiths Function: (Smith 1936)

Lp

I (0)e ke H

2
K Lb
I (0)e ke H

(110)

Steeles Equation (Steele 1962):

Lb

I (0)e ke H 1

e
K Lb

I ( 0) e ke H
K Lb

(111)

where KLb = the appropriate bottom algae light parameter for each light model.
Space Limitation. If a first-order growth model is used, a term must be included to
impose a space limitation on the bottom algae. A logistic model is used for this purpose
as in
Sb 1

ab
a b ,max

where ab,max = the carrying capacity [gD/m2].

Losses
Respiration. Bottom algae respiration is represented as a first-order rate that is
attenuated at low oxygen concentration,
BotAlgResp Foxb [k rb ,1 (T ) ab k rb , 2 BotAlgPhoto]

(112)

where krb,1(T) = temperature-dependent bottom algae basal respiration rate [/d], krb,2 =
bottom algae photo-respiration respiration rate constant [dimensionless], and Foxb =
attenuation due to low oxygen [dimensionless]. Laws and Chalup (1990) suggest a
typical basal respiration rate (krb,1) of about 0.042 d-1 and a photo-respiration rate constant
(krb,2) of about 0.389, which corresponds to about 39% of the actual growth rate (Chapra,
1997). Oxygen attenuation is modeled by Eqs. (111) to (113) with the oxygen
dependency represented by the parameter Ksob.

54

Death. Bottom algae death is represented as a first-order rate,

BotAlgDeath k db (T )ab

(113)

where kdb(T) = the temperature-dependent bottom algae death rate [/d].

Detritus (mo)
Detritus or particulate organic matter (POM) increases due to plant death. It is lost via
dissolution and settling
S mo rda PhytoDeath BotAlgDeath DetrDiss DetrSettl

(114)

where
DetrDiss k dt (T ) mo

(115)

where kdt(T) = the temperature-dependent detritus dissolution rate [/d] and

DetrSettl

v dt
mo
H

(116)

where vdt = detritus settling velocity [m/d].

Slowly Reacting CBOD (cs)

Slowly reacting CBOD increases due to detritus dissolution. It is lost via hydrolysis.
S cs rod DetrDiss SlowCHydr SlowCOxid

(117)

where
SlowCHydr k hc (T )c s

(118)

SlowCOxid Foxcf k dcs (T )c s

(119)

where khc(T) = the temperature-dependent slow CBOD hydrolysis rate [/d], kdcs(T) = the
temperature-dependent fast CBOD oxidation rate [/d] and Foxcf = attenuation due to low
oxygen [dimensionless].

Fast Reacting CBOD (cf)

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Fast reacting CBOD is gained via the hydrolysis of slowly-reacting CBOD. It is lost via
oxidation and denitrification.
S cf SlowCHydr FastCOxid rondn Denitr J CH4,d

Ast ,i
Vi

(120)

where
FastCOxid Foxcf k dc (T )c f

(121)

where kdc(T) = the temperature-dependent fast CBOD oxidation rate [/d] and Foxcf =
attenuation due to low oxygen [dimensionless]. The parameter rondn is the ratio of oxygen
equivalents lost per nitrate nitrogen that is denitrified (Eq. 69). The term Denitr is the rate
of denitrification [gN/L/d] defined in a later section. The term JCH4,d is the sediment flux
of dissolved methane in oxygen equivalents (gO2/m2/d) as described in a later section.
Three formulations are used to represent the oxygen attenuation:
Half-Saturation:
Foxrp

(122)

K socf o

where Ksocf = half-saturation constant for the effect of oxygen on fast CBOD oxidation
[mgO2/L].
Exponential:
Foxrp (1 e

K socf o

(123)

where Ksocf = exponential coefficient for the effect of oxygen on fast CBOD oxidation
[L/mgO2].
Second-Order Half Saturation:
Foxrp

o2
K socf o 2

(124)

where Ksocf = half-saturation constant for second-order effect of oxygen on fast CBOD
oxidation [mgO22/L2].

Organic Nitrogen (no)

Organic nitrogen increases due to plant death. It is lost via hydrolysis and settling.
56

S no rna PhytoDeath q N BotAlgDeath ONHydr ONSettl

(125)

The rate of organic nitrogen hydrolysis is computed as

ONHydr k hn (T ) n o

(126)

where khn(T) = the temperature-dependent organic nitrogen hydrolysis rate [/d].

ONSettl

v on
no
H

(127)

where von = organic nitrogen settling velocity [m/d].

Ammonia Nitrogen (na)

Ammonia nitrogen increases due to organic nitrogen hydrolysis and phytoplankton
respiration. It is lost via nitrification and plant photosynthesis:
S na ONHydr rna PhytoResp NH4Nitrif rna Pap PhytoPhoto
[J NH4 Pab BotAlgUptakeN ( NUpWCfrac)]

Ast ,i

(128)

Vi

The ammonia nitrification rate is computed as

NH4Nitrif Foxna k n (T ) n a

(129)

where kn(T) = the temperature-dependent nitrification rate for ammonia nitrogen [/d] and
Foxna = attenuation due to low oxygen [dimensionless]. Oxygen attenuation is modeled by
Eqs. (111) to (113) with the oxygen dependency represented by the parameter Ksona.
The coefficients Pap and Pab are the preferences for ammonium as a nitrogen source
for phytoplankton and bottom algae, respectively,
Pap

Pab

(k hnxp

n a k hnxp
na nn

n a )(k hnxp n n ) (n a n n )(k hnxp n n )

(130)

(k hnxb

na nn
n a k hnxb

n a )(k hnxb n n ) (n a n n )(k hnxb n n )

(131)

where khnxp = preference coefficient of phytoplankton for ammonium [mgN/m3] and khnxb =
preference coefficient of bottom algae for ammonium [mgN/m3].

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57

July 16, 2004

The fraction of N uptake from the water column by bottom plants is described by
NUpWCfrac. For periphyton, the value of NUpWCfrac is 1 since 100% of their nutrient
uptake occurs from the water column. For macrophytes the value of NUpWCfrac may be
less than 1.
The term JNH4 is the sediment flux of ammonia as described in a later section.

Unionized Ammonia
The model simulates total ammonia. In water, the total ammonia consists of two forms:
ammonium ion, NH4+, and unionized ammonia, NH3. At normal pH (6 to 8), most of the
total ammonia will be in the ionic form. However at high pH, unionized ammonia
predominates. The amount of unionized ammonia can be computed as
nau Fu na

(132)

where nau = the concentration of unionized ammonia [gN/L], and Fu = the fraction of the
total ammonia that is in unionized form,
Fu

1
1 10

pH

(133)

Ka

where Ka = the equilibrium coefficient for the ammonia dissociation reaction, which is
related to temperature by
pK a 0.09018

2729.92
Ta

(134)

where Ta is absolute temperature [K] and pKa = log10(Ka).

Nitrate Nitrogen (nn)

Nitrate nitrogen increases due to nitrification of ammonia. It is lost via denitrification and
plant photosynthesis:
S ni NH4Nitrif Denitr rna (1 Pap ) PhytoPhoto
[J NO3 (1 Pab ) BotAlgUptakeN(NUpWCfrac)]

Ast ,i

(135)

Vi

The denitrification rate is computed as

Denitr (1 Foxdn )k dn (T ) n n

(136)

58

where kdn(T) = the temperature-dependent denitrification rate of nitrate nitrogen [/d] and
Foxdn = effect of low oxygen on denitrification [dimensionless] as modeled by Eqs. (111)
to (113) with the oxygen dependency represented by the parameter Ksodn.
The fraction of N uptake from the water column by bottom plants is described by
NUpWCfrac. For periphyton, the value of NUpWCfrac is 1 since 100% of their nutrient
uptake occurs from the water column. For macrophytes the value of NUpWCfrac may be
less than 1.
The term JNO3 is the sediment flux of nitrate (mgN/m2/d) as described in a later section.

Organic Phosphorus (po)

Organic phosphorus increases due to plant death. It is lost via hydrolysis and settling.
S po rpa PhytoDeath q P BotAlgDeath OPHydr OPSettl

(137)

where the rate of organic phosphorus hydrolysis is computed as

OPHydr k hp (T ) p o

(138)

where khp(T) = the temperature-dependent organic phosphorus hydrolysis rate [/d].

Organic phosphorus settling is determined as
OPSettl

v op
H

(139)

po

where vop = organic phosphorus settling velocity [m/d].

Inorganic Phosphorus (pi)

Inorganic phosphorus increases due to organic phosphorus hydrolysis and phytoplankton
respiration. It is lost via plant photosynthesis. In addition, a settling loss is included for
cases in which inorganic phosphorus is lost due to sorption onto settleable particulate
matter such as iron oxyhydroxides:
S pi DOPHydr rpa PhytoResp rpa PhytoPhoto IPSettl
[J PO4 BotAlgUptakeP( PUpWCfrac) ]

Ast ,i

(140)

Vi

where

QUAL2K

59

July 16, 2004

IPSettl

v ip
H

(141)

pi

where vip = inorganic phosphorus settling velocity [m/d].

The fraction of P uptake from the water column by bottom plants is described by
PUpWCfrac. For periphyton, the value of PUpWCfrac is 1 since 100% of their nutrient
uptake occurs from the water column. For macrophytes the value of PUpWCfrac may be
less than 1.
The term JPO4 is the sediment flux of inorganic P (mgP/m2/d) as defined in a later section.

Inorganic Suspended Solids (mi)

Inorganic suspended solids are lost via settling,
Smi = InorgSettl
where
InorgSettl

vi
mi
H

(142)

where vi = inorganic suspended solids settling velocity [m/d].

Dissolved Oxygen (o)

Dissolved oxygen increases due to plant photosynthesis. It is lost via fast and slow
CBOD oxidation, nitrification and plant respiration, and oxidation of non-carbonaceous
non-nitrogenous chemical oxygen demand (COD). Depending on whether the water is
undersaturated or oversaturated it is gained or lost via reaeration,
S o roa (PhytoPhoto - PhytoResp) ro d (BotAlgPhoto - BotAlgResp)

Ast ,i
Vi

roc FastCOxid roc SlowCOxid ron NH4Nitr OxReaer CODoxid SOD

Ast ,i
Vi

(143)

where

OxReaer k a (T ) o s (T , elev) o

(144)

60

where ka(T) = the temperature-dependent oxygen reaeration coefficient [/d], os(T, elev) =
the saturation concentration of oxygen [mgO2/L] at temperature, T, and elevation above
sea level, elev. The term CODoxid is the COD oxidation (mgO2/L/d) as defined in the
section below on the generic constituent. SOD is the sediment oxygen demand [gO2/m2/d]
as described in a later section.
Oxygen Saturation
The following equation is used to represent the dependence of oxygen saturation on
temperature (APHA 1992)
ln o s (T , 0) 139.34411

1.575701 10 5 6.642308 10 7

Ta
Ta2

1.243800 10
Ta3

10

11

8.621949 10

(145)

Ta4

where os(T, 0) = the saturation concentration of dissolved oxygen in freshwater at 1 atm

[mgO2/L] and Ta = absolute temperature [K] where Ta = T +273.15.
The effect of elevation is accounted for by

o s (T , elev) e ln os (T , 0 ) (1 0.0001148elev)

(146)

Reaeration Formulas
The reaeration coefficient (at 20 oC) can be prescribed on the Reach Worksheet. If
reaeration is not prescribed (that is, it is blank or zero for a particular reach), it is computed
as a function of the rivers hydraulics and (optionally) wind velocity,
k a ( 20) k ah ( 20)

K Lw ( 20)
H

(147)

where kah(20) = the reaeration rate at 20 oC computed based on the rivers hydraulic
characteristics [d1], KL(20) = the reaeration mass-transfer coefficient based on wind
velocity [m/d], and H = mean depth [m].
Hydraulic-based Formulas:
OConnor-Dobbins (OConnor and Dobbins 1958):
k ah ( 20) 3.93

QUAL2K

U 0.5
H 1.5

(148)

61

July 16, 2004

where U = mean water velocity [m/s] and H = mean water depth [m].
Churchill (Churchill et al. 1962):
k ah ( 20) 5.026

U
H 1.67

(149)

Owens-Gibbs (Owens et al. 1964):

k ah ( 20) 5.32

U 0.67
H 1.85

(150)

Tsivoglou-Neal (Tsivoglou and Neal 1976):

Low flow, Q = 0.0283 to 0.4247 cms (1 to 15 cfs):
k ah (20) 31,183 US

(151)

High flow, Q = 0.4247 to 84.938 cms (15 to 3000 cfs):

k ah ( 20) 15,308 US

(152)

where S = channel slope [m/m].

Thackston-Dawson (Thackston and Dawson 2001):
k ah ( 20) 2.16(1 9 F 0.25 )

U*
H

(153)

where U* = shear velocity [m/s], and F = the Froude number [dimensionless]. The shear
velocity and the Froude number are defined as
U*

gR h S

(154)

and
F

U
gH d

(155)

where g = gravitational acceleration (= 9.81 m/s2), Rh = hydraulic radius [m], S = channel

slope [m/m], and Hd = the hydraulic depth [m]. The hydraulic depth is defined as
Hd

Ac
Bt

(156)

62

where Bt = the top width of the channel [m].

USGS (Pool-riffle) (Melching and Flores 1999):
Low flow, Q < 0.556 cms (< 19.64 cfs):
k ah (20) 517(US ) 0.524 Q 0.242

(157)

High flow, Q > 0.556 cms (> 19.64 cfs):

k ah (20) 596(US ) 0.528 Q 0.136

(158)

where Q = flow (cms).

USGS (Channel-control) (Melching and Flores 1999):
Low flow, Q < 0.556 cms (< 19.64 cfs):
k ah (20) 88(US ) 0.313 H 0.353

(159)

High flow, Q > 0.556 cms (> 19.64 cfs):

k ah ( 20) 142(US ) 0.333 H 0.66 Bt0.243

(160)

Internal (Covar 1976):

Reaeration can also be internally calculated based on the following scheme patterned
after a plot developed by Covar (1976) (Figure 19):
If H < 0.61 m, use the Owens-Gibbs formula
If H > 0.61 m and H > 3.45U2.5, use the OConnor-Dobbins formula
Otherwise, use the Churchill formula
This is referred to as option Internal on the Rates Worksheet of Q2K. Note that if no
option is specified, the Internal option is the default.

QUAL2K

63

July 16, 2004

10

OConnor
Dobbins
0.05
0.1
Churchill

Depth (m)

0.2
0.5
1

2
5
10
20
50
100

0.1
0.1

Owens
Gibbs

Velocity (mps)

Figure 19 Reaeration rate (/d) versus depth and velocity (Covar 1976).

Wind-based Formulas:
Three options are available to incorporate wind effects into the reaeration rate: (1) it can
be omitted, (2) the Banks-Herrera formula and (3) the Wanninkhof formula.
Banks-Herrera formula (Banks 1975, Banks and Herrera 1977):
K lw 0.728U w0.,510 0.317U w,10 0.0372U w2 ,10

(161)

where Uw,10 = wind speed measured 10 meters above the water surface [m s1]
Wanninkhof formula (Wanninkhof 1991):
1.64
K lw 0.0986U w
,10

(162)

Note that the model uses Eq. (50) to correct the wind velocity entered on the
Meteorology Worksheet (7 meters above the surface) so that it is scaled to the 10-m
height.
Effect of Control Structures: Oxygen
Oxygen transfer in streams is influenced by the presence of control structures such as
weirs, dams, locks, and waterfalls (Figure 20). Butts and Evans (1983) have reviewed
efforts to characterize this transfer and have suggested the following formula,
rd 1 0.38a d bd H d (1 0.11H d )(1 0.046T )

(163)

64

where rd = the ratio of the deficit above and below the dam, Hd = the difference in water
elevation [m] as calculated with Eq. (7), T = water temperature (C) and ad and bd are
coefficients that correct for water-quality and dam-type.
Values of ad and bd are summarized in Table 7. At present, Q2K uses the following
values for these coefficients: ad = 1.25 and bd = 0.9.

Qi1 oi1
Qi1 oi1

Hd

i1

Figure 20 Water flowing over a river control structure.

Table 7 Coefficient values used to predict the effect of dams on stream reaeration.

(a) Water-quality coefficient

Polluted state
Gross
Moderate
Slight
Clean
(b) Dam-type coefficient
Dam type
Flat broad-crested regular step
Flat broad-crested irregular step
Flat broad-crested vertical face
Flat broad-crested straight-slope
face
Flat broad-crested curved face
Round broad-crested curved face
Sharp-crested straight-slope face
Sharp-crested vertical face
Sluice gates

ad
0.65
1.0
1.6
1.8
bd
0.70
0.80
0.60
0.75
0.45
0.75
1.00
0.80
0.05

The oxygen mass balance for the reach below the structure is written as

QUAL2K

65

July 16, 2004

Qab,i
Wo ,i
doi Qi 1
Q
E'

o'i 1 i oi
oi i oi 1 oi
S o ,i
dt
Vi
Vi
Vi
Vi
Vi

(164)

where oi1 = the oxygen concentration entering the reach [mgO2/L], where
o'i 1 o s ,i 1

o s ,i 1 oi 1

(165)

rd

Pathogen (x)
Pathogens are subject to death and settling,
S x PathDeath PathSettl

(166)

Death
Pathogen death is due to natural die-off and light (Chapra 1997). The death of pathogens
in the absence of light is modeled as a first-order temperature-dependent decay and the
death rate due to light is based on the Beer-Lambert law,
PathDeath k dx (T ) x path

I (0) / 24
1 e ke H x
ke H

(167)

where kdx(T) = temperature-dependent pathogen die-off rate [/d] and path is a constant for
the light-induced mortality (day-1 per ly/hour). Thomann and Mueller (1987) suggest that
path is a approximately unity.
Settling
Pathogen settling is represented as
PathSettl

vx
x
H

(168)

where vx = pathogen settling velocity [m/d].

Generic constituent (gen)

A generic constituent is available for optional use. The user has the option of either
assuming that the generic constituent has no interaction with other state variables, or it
can be treated as a non-carbonaceous non-nitrogenous chemical oxygen demand (COD).
The generic constituent is also subject to first-order decay and settling,
66

S gen k gen (T ) gen

v gen
H

(169)

gen

where kgen(T) = temperature-dependent decay rate [/d] and vgen = settling velocity [m/d].
If the generic constituent is used as COD, then the COD oxidation rate (mgO2/L/d) is
determined by
CODoxid k gen (T ) gen

(170)

where gen is in units of mgO2/L.

pH
The following equilibrium, mass balance and electroneutrality equations define a
freshwater dominated by inorganic carbon (Stumm and Morgan 1996),
K1

K2

[ HCO 3 ][H ]

(171)

[ H 2 CO *3 ]

[CO 32 ][H ]

(172)

[HCO 3 ]

K w [H ][OH ]

(173)

cT [ H 2 CO *3 ] [HCO 3 ] [CO 32 ]

(174)

Alk [HCO 3 ] 2[CO 32 ] [OH ] [H ]

(175)

where K1, K2 and Kw are acidity constants, Alk = alkalinity [eq L1], H2CO3* = the sum of
dissolved carbon dioxide and carbonic acid, HCO3 = bicarbonate ion, CO32 = carbonate
ion, H+ = hydronium ion, OH = hydroxyl ion, and cT = total inorganic carbon
concentration [mole L1]. The brackets [ ] designate molar concentrations.
Note that the alkalinity is expressed in units of eq/L for the internal calculations. For
input and output, it is expressed as mgCaCO3/L. The two units are related by
Alk ( mgCaCO 3 /L) 50,000 Alk (eq/L)

(176)

The equilibrium constants are corrected for temperature by

QUAL2K

67

July 16, 2004

Harned and Hamer (1933):

pK w =

4787.3
7.1321 log10 (Ta ) 0.010365Ta 22.80
Ta

(177)

Plummer and Busenberg (1982):

logK1 = 356.3094 0.06091964Ta 21834.37 / Ta

126.8339 log Ta 1,684,915 / Ta2

(178)

Plummer and Busenberg (1982):

logK 2 = 107.8871 0.03252849Ta 5151.79 / Ta

38.92561 log Ta 563,713.9 / Ta2

(179)

The nonlinear system of five simultaneous equations (158 through 162) can be solved
numerically for the five unknowns: [H2CO3*], [HCO3], [CO32], [OH], and {H+}. An
efficient solution method can be derived by combining Eqs. (158), (159) and (161) to
define the quantities (Stumm and Morgan 1996)
0

[H ] 2

(180)

[H ] 2 K1[H ] + K1 K 2

K1[H ]

(181)

[H ] 2 K1[H ] + K1 K 2

K1 K 2

(182)

[H ] K1[H ] + K1 K 2

where 0, 1, and 2 = the fraction of total inorganic carbon in carbon dioxide,

bicarbonate, and carbonate, respectively. Equations (160), (162), (168) and (169) can then
be combined to yield,
Alk = ( 1 2 2 )cT

Kw

[H ]

[H ]

(183)

Thus, solving for pH reduces to determining the root, {H+}, of

f ([H ]) = ( 1 2 2 )cT

Kw
[H ]

[H ] Alk

(184)

68

where pH is then calculated with

pH log10 [ H ]

(185)

The root of Eq. (155) is determined with a numerical method. The user can choose
either the Newton-Raphson or the bisection method (Chapra and Canale 2002) as
specified on the QUAL2K sheet. The Newton-Raphson is faster and is the default
method. However, it can sometimes diverge. In such cases, because it is more stable, the
bisection method would be preferable.

Total Inorganic Carbon (cT)

Total inorganic carbon concentration increases due to fast carbon oxidation and plant
respiration. It is lost via plant photosynthesis. Depending on whether the water is
undersaturated or oversaturated with CO2, it is gained or lost via reaeration,
S cT rcco FastCOxid rcca (PhytoResp PhytoPhoto)
rccd (BotAlgResp BotAlgPhoto)

Ast ,i
Vi

CO2Reaer

(186)

where

CO2Reaer k ac (T ) [CO 2 ] s 0 cT

(187)

where kac(T) = the temperature-dependent carbon dioxide reaeration coefficient [/d], and
[CO2]s = the saturation concentration of carbon dioxide [mole/L].
The stoichiometric coefficients are derived from Eq. (60)6
gC
moleC
m3

12 gC 1000 L
mgA

(188)

gC
moleC
m3

12 gC 1000 L
gD

(189)

gC

gO 2

(190)

rcca rca

rccd rcd

rcco

1
roc

moleC
m3

12 gC 1000 L

Carbon Dioxide Saturation

6

The conversion, m3 = 1000 L is included because all mass balances express volume in m3, whereas total
inorganic carbon is expressed as mole/L.

QUAL2K

69

July 16, 2004

The CO2 saturation is computed with Henrys law,

[CO 2 ]s K H p CO2

(191)

where KH = Henry's constant [mole (L atm)1] and pCO2 = the partial pressure of carbon
dioxide in the atmosphere [atm]. Note that the partial pressure is input on the Rates
Worksheet in units of ppm. The program internally converts ppm to atm using the
conversion: 106 atm/ppm.
The value of KH can be computed as a function of temperature by (Edmond and
Gieskes 1970)
pK H =

2385.73
0.0152642Ta 14.0184
Ta

(192)

The partial pressure of CO2 in the atmosphere has been increasing, largely due to the
combustion of fossil fuels (Figure 21). Values in 2003 are approximately 103.43 atm (=
372 ppm).

Figure 21 Concentration of carbon dioxide in the atmosphere as recorded at Mauna Loa

Observatory, Hawaii. (http://www.cmdl.noaa.gov/ccg/figures/co2mm_mlo.jpg).

CO2 Gas Transfer

70

The CO2 reaeration coefficient can be computed from the oxygen reaeration rate by
32

44

k ac ( 20)

0.25

(193)

k a ( 20) 0.923 k a ( 20)

Effect of Control Structures: CO2

As was the case for dissolved oxygen, carbon dioxide gas transfer in streams can be
influenced by the presence of control structures. Q2K assumes that carbon dioxide
behaves similarly to dissolved oxygen (recall Sec. ). Thus, the inorganic carbon mass
balance for the reach immediately downstream of the structure is written as
Qab,i
WcT ,i
Qi 1
Qi
Ei'

c'T ,i 1
cT ,i
cT ,i
cT ,i 1 cT ,i
S cT ,i
dt
Vi
Vi
Vi
Vi
Vi

dcT ,i

(194)

where c'T,i1 = the concentration of inorganic carbon entering the reach [mgO2/L], where
c'T ,i 1 ( 1 2 )cT ,i 1 CO2, s ,i 1

CO2 , s ,i 1 0 cT ,i 1

(195)

rd

where rd is calculated with Eq. (152).

Alkalinity (Alk)
The present model accounts for changes in alkalinity due to plant photosynthesis and
respiration, nitrogen and phosphorus hydrolysis, nitrification, and denitrification.
S alk ralkaa Pap ralkan (1 Pap ) PhytoPhoto ralkaa PhytoResp
ralkbn ONHydr ralkbp OPHydr ralkn NH4Nitr ralkden Denitr
[ralkbn (1 Pap )BotAlgUptakeN ralkbn Pap BotAlgUptakeN ralkbp BotAlgUptakeP]

Ast ,i
Vi

(196)

where the rs are ratios that translate the processes into the corresponding amount of
alkalinity. The stoichiometric coefficients are derived from Eqs. (60) through (63) as in
Phytoplankton Photosynthesis (Ammonia as Substrate) and Respiration:
gC
14 eqH
moleC
m3

106 moleC 12 gC 1000 L

mgA

ralkaa rca

(197)

Phytoplankton Photosynthesis (Nitrate as Substrate):

QUAL2K

71

July 16, 2004

gC
18 eqH
moleC
m3

106 moleC 12 gC 1000 L

mgA

ralkan rca

(198)

Bottom Algae Nitrogen Uptake and Nitrogen Hydrolysis:

ralkbn

16 eqH
moleN
gN
m3

16 moleN 14 gN
1000 mgN 1000 L

(199)

Bottom Algae Phosphorus Uptake and Phosphorus Hydrolysis:

ralkbp

2 eqH
moleP
gP
m3

1 moleP
31 gP
1000 mgP 1000 L

(200)

Nitrification:
ralkn

2 eqH
1 gN
moleN
1 m3

1 moleN
14 gN
1000 mgN 1000 L

(201)

Denitrification:
ralkden

4 eqH
1 gN
moleN
1 m3

1 moleN
14 gN
1000 mgN 1000 L

(202)

Constituent Reactions in the Hyporheic Pore Water

(Level 1)
The Level 1 option in Q2K for constituents in the hyporheic pore water includes
simulation of zero-order or first-order oxidation of fast-reacting dissolved CBOD with
attenuation from temperature, CBOD, and dissolved oxygen. The Level 1 option does not
include simulation of the biofilm of heterotrophic bacteria as a state variable. Instead, the
net growth of the biofilm is estimated from the input of either a zero-order or first-order
oxidation rate of fast-reacting CBOD that is attenuated by temperature, dissolved oxygen,
and fast-reacting CBOD concentrations.
The mathematical relationships that describe the individual reactions and concentrations
of the model state variables (Table 5) for Level 1 simulation of water quality constituents
in the hyporheic pore water are presented in the following paragraphs.

Conservative Substance (s)

By definition, conservative substances are not subject to reactions. Therefore the net gain
or loss in the hyporheic sediment zone (Ss,2) is calculated as

72

(203)

Ss,2 = 0

Phytoplankton (ap)
Phytoplankton are lost via respiration and death. The net gain or loss in the hyporheic
sediment zone (Sap,2) is calculated as
S ap , 2 PhytoResp2 PhytoDeath 2

(204)

Losses
Respiration. Phytoplankton respiration is represented as a first-order rate that is
attenuated at low oxygen concentration. Phytoplankton respiration in the hyporheic
sediment zone is calculated as
PhytoResp2 Foxrp , 2 k rp (T ) a p , 2

(205)

where krp(T) = temperature-dependent phytoplankton respiration rate [/d] (Ti,2 is used for
temperature adjustment of all rates in the hyporheic sediment zone of a reach) and Foxrp,2
= attenuation in the hyporheic zone due to low oxygen. Three formulations are used to
represent the oxygen attenuation (o2 is used to determine oxygen attenuation in the
hyporheic pore water zone).
Death. Phytoplankton death is represented as a first-order rate. Death in the hyporheic
sediment zone is calculated as
PhytoDeath 2 k dp (T ) a p , 2

(206)

where kdp(T) = temperature-dependent phytoplankton death rate [/d].

Net growth of heterotrophic bacteria in the hyporheic sediment

The Level 1 option of Q2K does not include simulation of the biofilm of heterotrophic
bacteria (aerobic bacteria) as a state variable. Instead, the net growth of attached
heterotrophic bacteria is estimated from the input of either a zero-order or first-order
oxidation rate of fast-reacting CBOD that is attenuated by temperature, dissolved oxygen,
and fast-reacting CBOD concentrations. The Rates sheet of Q2K allows the user to select
either a zero-order or first-order oxidation rate model, and specify the appropriate zeroorder or first-order oxidation rates. If a zero-order oxidation rate is selected on the Rates
sheet, then the following equation represents the net growth rate of heterotrophic
bacteria:
HeteroGrow C gh (T ) Nh rdo

QUAL2K

(207)

73

July 16, 2004

where Cgh(T) = the temperature-dependent oxidation rate of fast-reacting CBOD by the

attached heterotrophic bacteria [as gO2m-2d-1)], and Nh = the attenuation factor due to the
concentration of fast-reacting CBOD and dissolved oxygen [dimensionless number
between 0 and 1], and rdo is the stoichiometric ratio between dry weight of organic
material in bacteria and oxygen [g dry weight/gO2] as discussed in the water column
section on Stoichiometry of Organic Matter.
If a first-order oxidation rate is specified on the Rates sheet, then the following equation
is used to represent the net growth rate of heterotrophic bacteria:
HeteroGrow k gh (T ) Nh c f , 2 rdo

V2 , i
Ast ,i

(208)

where kgh(T) = the maximum oxidation rate of fast-reacting CBOD at temperature T due
to the net growth of attached heterotrophic bacteria [d-1], and Nh = the attenuation factor
due to the concentration of fast-reacting CBOD and dissolved oxygen [dimensionless
number between 0 and 1], cf,2 is the concentration of fast-reacting CBOD in the hyporheic
pore water [gO2/m3], rdo is the stoichiometric ratio between dry weight and oxygen
equivalents [g dry weight/gO2], V2,i is the volume of hyporheic pore water in reach i [m3],
and Ast,i is the surface area of reach i [m2].
Temperature Effect. As for the first-order reactions described in the water column
section on Temperature Effects on Reactions, an Arrhenius model is employed to quantify
the effect of temperature if a zero-order oxidation model is selected:
C gh (T ) C h ( 20) T 20

(209)

Nutrient and Substrate Limitation. Michaelis-Menten equations are used to represent the
attenuation of oxidation due to fast-reacting CBOD. Three formulations are used to
represent the oxygen attenuation (o2 is used to determine oxygen attenuation in the
hyporheic zone). The minimum value is then used to compute the nutrient attenuation
coefficient,

Nh min

c f ,2

k c
f ,2
sCh

, Foxrh

(210)

where ksNh = nitrogen half-saturation constant [gN/L] and ksPh = phosphorus halfsaturation constant [gP/L], k sCh = fast-reacting dissolved CBOD half-saturation
constant (mgO2/L), and Foxrh = the oxygen attenuation factor [dimensionless number
between 0 and 1].

Detritus (mo)

74

Detritus or particulate organic matter (POM) increases due to phytoplankton death. It is

lost from the hyporheic pore water via dissolution. The net gain or loss from the
hyporheic sediment zone (Smo,2) is calculated as
S mo , 2 rda PhytoDeath 2 DetrDiss 2

(211)

where
DetrDiss 2 k dc (T ) mo , 2

(212)

where kdc(T) = the temperature-dependent detritus dissolution rate [/d].

Slow-reacting CBOD (cs)

Slow-reacting CBOD increases due to detritus dissolution. It is lost via hydrolysis. The
net gain or loss in the hyporheic sediment zone (Scs,2) is calculated as
S cs , 2 rcd DetrDiss 2 SlowCHydr2 SlowCOxid 2

(213)

where
SlowCHydr2 k hc (T )cs , 2

(214)

SlowCOxid 2 Foxcf k dcs (T )c s , 2

(215)

where khc(T) = the temperature-dependent slow CBOD hydrolysis rate [/d], kdcs(T) = the
temperature-dependent fast CBOD oxidation rate [/d] and Foxcf = attenuation due to low
oxygen [dimensionless].

Fast-reacting CBOD (cf)

Fast-reacting CBOD is gained via the hydrolysis of slowly-reacting CBOD. It is lost via
oxidation by suspended bacteria, oxidation from the net growth of the biofilm of
heterotrophic bacteria, and denitrification. The net gain or loss from the hyporheic
sediment zone (Scf,2) is calculated as
S cf , 2 SlowCHydr2 FastCOxid 2 rod HeteroGrow

Ast ,i
V2 ,i

rondn Denitr2

(216)

The oxidation by suspended bacteria in the hyporheic sediment zone is represented as

FastCOxid 2 Foxcf , 2 kcf (T )c f , 2

(217)

where kcf(T) = the temperature-dependent fast carbon oxidation rate [/d] and Foxcf =
attenuation due to low oxygen [dimensionless]. Oxygen attenuation (Foxcf) is represented
with the oxygen dependency represented by the parameter Ksocf with o2 in the hyporheic
QUAL2K

75

July 16, 2004

zone. The parameter rondn is the ratio of oxygen equivalents of carbon lost per nitrate
nitrogen that is denitrified. The term Denitr is the rate of denitrification [gN/L/d]. It
will be defined in the water column section on Nitrate Nitrogen.

Organic Nitrogen (no)

Organic nitrogen increases due to detritus dissolution. It is lost via hydrolysis. The net
gain or loss from the hyporheic sediment zone (Sno,2) is calculated as
S no , 2 rnd DetrDiss 2 ONHydr2

(218)

The hydrolysis rate is calculated as

ONHydr2 k hn (T )no , 2

(219)

where khn(T) = the temperature-dependent organic nitrogen hydrolysis rate [/d].

Ammonia Nitrogen (na)

Ammonia nitrogen increases due to organic nitrogen hydrolysis and respiration of
phytoplankton. It is lost via nitrification. The net gain or loss from the hyporheic
sediment zone (Sna,2) is calculated as
S na , 2 ONHydr2 rna PhytoResp 2 NH4Nitrif 2

(220)

The ammonia nitrification rate is computed as

NH4Nitrif 2 Foxna , 2 k na (T ) na , 2

(221)

where kna(T) = the temperature-dependent nitrification rate for ammonia nitrogen [/d] and
Foxna = attenuation due to low oxygen [dimensionless]. Oxygen attenuation is modeled
with the oxygen dependency represented by the parameter Ksona.

Nitrate Nitrogen (nn)

Nitrate nitrogen increases due to nitrification of ammonia. It is lost via denitrification.
The net gain or loss from the hyporheic sediment zone (Snn,2) is calculated as
S nn , 2 NH4Nitrif 2 Denitr2

(222)

The denitrification rate is computed as

Denitr2

c f ,2
0 .1 c f , 2

(1 Foxdn , 2 )k dn (T )nn , 2

(223)

76

where kdn(T) = the temperature-dependent denitrification rate of nitrate nitrogen [/d] and
Foxdn = effect of low oxygen on denitrification [dimensionless] as modeled with the
oxygen dependency represented by the parameter Ksodn.

Organic Phosphorus (po)

Organic phosphorus increases due to dissolution of detritus. It is lost via hydrolysis. The
net gain or loss for the hyporheic sediment zone (Spo,2) is calculated as
S po , 2 rpd DetrDiss 2 OPHydr2

(224)

where
OPHydr2 k hp (T ) po , 2

(225)

where khp(T) = the temperature-dependent organic phosphorus hydrolysis rate [/d].

Inorganic Phosphorus (pi)

Inorganic phosphorus in the hyporheic sediment zone increases due to organic
phosphorus hydrolysis and respiration of phytoplankton. The net gain in the hyporheic
sediment zone (Spi,2) is calculated as
S pi , 2 OPHydr2 rpa PhytoResp 2

(226)

Dissolved Oxygen (o)

Dissolved oxygen is lost via oxidation of fast and slow CBOD by suspended bacteria, and
the net effect of growth and respiration of heterotrophic bacteria. It is also lost due to
nitrification, phytoplankton respiration, and oxidation of non-carbonaceous nonnitrogenous chemical oxygen demand (COD). The loss of dissolved oxygen from the
hyporheic sediment zone (So,2) is calculated as
S o , 2 SlowCOxid 2 FastCOxid 2 rod HeteroGrow

Ast ,i
V2,i

ron NH4Nitr2 roa PhytoResp 2 CODoxid 2

(227)
The term CODoxid2 is the COD oxidation (mgO2/L/d) as defined in the section below on
the generic constituent.

Pathogen (x)

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Pathogens are subject to death in the hyporheic sediment zone. The loss in the hyporheic
zone (Sx,2) is computed as
S x , 2 PathDeath 2

(228)

Pathogen death is due to natural die-off. The death of pathogens in the absence of light is
modeled as a first-order temperature-dependent decay,
PathDeath 2 k dx (T ) x2

(229)

where kdx(T) = temperature-dependent pathogen die-off rate [/d].

Generic constituent (gen)

A generic constituent is available for optional use. The user has the option of either
assuming that the generic constituent has no interaction with other state variables, or it
can be treated as a non-carbonaceous non-nitrogenous chemical oxygen demand (COD).
The generic constituent is also subject to first-order decay and settling in the hyporheic
zone,
S gen , 2 k gen (T ) gen2

(230)

where kgen(T) = temperature-dependent decay rate [/d].

If the generic constituent is used as COD, then the COD oxidation rate (mgO2/L/d) is
determined by
CODoxid 2 k gen (T ) gen

(231)

where gen is in units of mgO2/L.

pH
The equilibrium, mass balance, and electroneutrality equations described in the water
column section on pH are used to determine the pH in the hyporheic pore water.

Total Inorganic Carbon (cT)

Total inorganic carbon concentration (cT) increases due to fast carbon oxidation from
suspended bacteria and the net growth of heterotrophic bacteria. It is also gained due to
the respiration of phytoplankton. The net gain in the hyporheic sediment zone (ScT,2) is
calculated as

78

S cT , 2 rcco SlowCOxid 2 rcco FastCOxid 2

rccd HeteroGrow

Ast ,i
V 2 ,i

(232)

rcca PhytoResp 2

The stoichiometric coefficients are derived in the water column section on Total
Inorganic Carbon.

Alkalinity (Alk)
Changes in alkalinity in the hyporheic zone are due to phytoplankton respiration,
nitrification, and denitrification. The net gain or loss for the hyporheic sediment zone
(Salk,2) is calculated as
S alk , 2 ralkaa PhytoResp 2 ralkn NH4Nitr2 ralkdn Denitr2

(233)

where the rs are ratios that translate the processes into the corresponding amount of
alkalinity. The stoichiometric coefficients are derived the water column section on in
Alkalinity.

Constituent Reactions in the Hyporheic Pore Water

(Level 2)
The metabolism of microbial assemblages in the hyporheic zones of streams and rivers
can influence the concentrations of nutrients, carbon, and dissolved oxygen of the
overlying water column. Naegeli and Uehlinger (1997) reported hyporheic respiration
rates that ranged from 3.9 to 5.9 g O2 m-2 d-1 and contributed 76-96% of the whole
ecosystem respiration in a sixth-order gravel bed river in Switzerland. Grimm and Fisher
(1984) found that respiration in hyporheic sediments accounted for at least half of the
whole ecosystem respiration in a fourth-order Arizona stream. Mulholland et al. (1997)
showed that ecosystem respiration rates and nutrient uptake rates are strongly correlated
with the rate of water exchange between the surface water and the hyporheic transient
storage zone.
The organic matter in the hyporheic zones can be attributed to three main pools: plant
tissue, biofilm, and sediment fauna (Spacil and Rulik, 1997). Biofilms of heterotrophic
bacteria typically make up most of the biomass of the hyporheic community (Leichtfried,
1988, 1991). The growth of heterotrophic biofilms involves the consumption of organic
carbon, uptake of nutrients and dissolved oxygen, and excretion of inorganic carbon.
Endogenous respiration of heterotrophic organisms involves uptake of dissolved oxygen
and excretion of nutrients. Death of heterotrophic organisms contributes to the detritus
(POM) in the ecosystem.
The Level 2 option in Q2K includes simulation of heterotrophic bacteria biofilm growth
(zero-order or first-order), respiration, and death, with attenuation of growth from
QUAL2K

79

July 16, 2004

temperature, DOC, dissolved oxygen, ammonia, nitrate, and inorganic phosphorus. The
Level 2 option simulates the biofilm concentration of heterotrophic bacteria in the
hyporheic zone as a state variable.
The mathematical relationships that describe the individual reactions and concentrations
of the model state variables (Table 5) for Level 2 simulation of water quality constituents
in the hyporheic pore water are presented in the following paragraphs.

Conservative Substance (s)

By definition, conservative substances are not subject to reactions. Therefore the net gain
or loss in the hyporheic sediment zone (Ss,2) is calculated as
Ss,2 = 0

(234)

Phytoplankton (ap)
Phytoplankton are lost via respiration and death. The net gain or loss in the hyporheic
sediment zone (Sap,2) is calculated as
S ap , 2 PhytoResp2 PhytoDeath 2

(235)

Losses
Respiration. Phytoplankton respiration is represented as a first-order rate that is
attenuated at low oxygen concentration. Phytoplankton respiration in the hyporheic
sediment zone is calculated as
PhytoResp2 Foxrp , 2 k rp (T ) a p , 2

(236)

where krp(T) = temperature-dependent phytoplankton respiration rate [/d] (Ti,2 is used for
temperature adjustment of all rates in the hyporheic sediment zone of a reach) and Foxrp,2
= attenuation in the hyporheic zone due to low oxygen. Three formulations are used to
represent the oxygen attenuation (o2 is used to determine oxygen attenuation in the
hyporheic zone).
Death. Phytoplankton death is represented as a first-order rate. Death in the hyporheic
sediment zone is calculated as
PhytoDeath 2 k dp (T ) a p , 2

(237)

where kdp(T) = temperature-dependent phytoplankton death rate [/d].

Heterotrophic bacteria in the hyporheic sediment (ah)

80

The Level 2 option of Q2K includes simulation of the biofilm of heterotrophic (aerobic)
bacteria as a state variable. Heterotrophic bacteria in the hyporheic sediment zone grow
due to the uptake of fast-reacting dissolved organic carbon. This functional group of
bacteria utilizes oxygen in their growth and respiration and represents a diverse crosssection of microorganisms. They are lost via respiration and death.
S ah HeteroGrow HeteroResp HeteroDeath

(238)

Growth
The representation of the growth of the heterotrophic bacteria is an adaptation of a model
developed by Rutherford et al. (1999). Growth is based on a temperature-corrected, zeroorder or first-order rate attenuated by nutrient and substrate concentrations. The Rates
sheet of QUAL2Kw allows the user to select either a zero-order or first-order growth rate
model, and the appropriate maximum growth rates are entered on the Reach sheet. If a
zero-order growth model is selected on the Rates sheet, then the following equations
represent the growth rate:
HeteroGrow C gh (T ) Nh rdo

(239)

where Cgh(T) = the temperature-dependent maximum growth rate of the biofilm of

heterotrophic bacteria [in terms of the equivalent amount of oxygen oxidized gO2m-2 d-1)],
and Nh = the heterotrophic bacteria nutrient/substrate attenuation factor [dimensionless
number between 0 and 1].
If a first-order growth rate is specified on the Rates sheet, then the following equation is
used to represent growth:
HeteroGrow k gh (T ) Nh Sh a h

(240)

where khb(T) = the maximum growth rate of the biofilm of heterotrophic bacteria at
temperature T [d-1], and Nh = the heterotrophic bacteria nutrient/substrate attenuation
factor [dimensionless number between 0 and 1], and Sh = biofilm space limitation
attenuation factor.
Temperature Effect. As for the first-order reactions described in the water column
section on Temperature Effects on Reactions, an Arrhenius model is employed to quantify
the effect of temperature if a zero-order growth model is selected:
C gh (T ) C h ( 20) T 20

(241)

Nutrient and Substrate Limitation. Michaelis-Menten equations are used to represent

growth limitation due to inorganic nitrogen and phosphorus, fast-reacting CBOD, and
oxygen attenuation. Three formulations are used to represent the oxygen attenuation (o2

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81

July 16, 2004

is used to determine oxygen attenuation in the hyporheic zone). The minimum value is
then used to compute the nutrient attenuation coefficient,

c f ,2
na , 2 nn , 2
pi , 2
,
,
, Foxrh
k n n

a ,2
n , 2 k sPh pi , 2 k sCh c f , 2
sNh

Nh min

(242)

where ksNh = nitrogen half-saturation constant [gN/L] and ksPh = phosphorus halfsaturation constant [gP/L], k sCh = fast-reacting CBOD half-saturation constant
(mgO2/L), and Foxrh = the oxygen attenuation factor [dimensionless number between 0 and
1].
Space Limitation. If a first-order growth model is used, a term must be included to
impose a space limitation on the biomass of heterotrophic biofilm. A logistic model is
used for this purpose as in

Sh 1

ah
ah ,max

where ab,max = the carrying capacity [gD/m2].

Losses
Respiration. Endogenous respiration of heterotrophic bacteria is represented as a firstorder rate that is attenuated at low oxygen concentration,
HeteroResp Foxrh k rh (T ) ah

(243)

where krh(T) = temperature-dependent heterotrophic bacteria respiration rate [/d] and Foxrh
= attenuation due to low oxygen [dimensionless].
Death. Heterotrophic bacteria death is represented as a first-order rate,
HeteroDeath k dh (T )ah

(244)

where kdh(T) = the temperature-dependent heterotrophic bacteria death rate [/d].

Detritus (mo)
Detritus or particulate organic matter (POM) increases due to plant or bacteria death. It is
lost from the hyporheic pore water via dissolution. The net gain or loss from the
hyporheic sediment zone (Smo,2) is calculated as

82

S mo, 2 rda PhytoDeath 2 HeteroDeath

Ast ,i
V2 , i

DetrDiss 2

(245)

where
DetrDiss 2 k dc (T ) mo , 2

(246)

where kdc(T) = the temperature-dependent detritus dissolution rate [/d].

Slow-reacting CBOD (cs)

Slow-reacting carbon increases due to detritus dissolution. It is lost via hydrolysis. The
net gain or loss in the hyporheic sediment zone (Scs,2) is calculated as
S cs , 2 rcd DetrDiss 2 SlowCHydr2 SlowCOxid 2

(247)

where
SlowCHydr2 k hc (T )cs , 2

(248)

SlowCOxid 2 Foxcf k dcs (T )c s , 2

(249)

where khc(T) = the temperature-dependent slow CBOD hydrolysis rate [/d], kdcs(T) = the
temperature-dependent fast CBOD oxidation rate [/d] and Foxcf = attenuation due to low
oxygen [dimensionless].

Fast-reacting CBOD (cf)

Fast-reacting carbon is gained via the hydrolysis of slowly-reacting carbon. It is lost via
oxidation by suspended bacteria, oxidation from the growth of the biofilm of
heterotrophic bacteria, and denitrification. The net gain or loss from the hyporheic
sediment zone (Scf,2) is calculated as
S cf , 2 SlowCHydr2 FastCOxid 2 rod HeteroGrow

Ast ,i
V2 ,i

rondn Denitr2

(250)

The oxidation of carbon by suspended bacteria in the hyporheic sediment zone is

represented as
FastCOxid 2 Foxrh k cf (T )c f , 2

(251)

where kcf(T) = the temperature-dependent fast carbon oxidation rate [/d] and Foxrh =
attenuation due to low oxygen [dimensionless]. The parameter rondn is the ratio of oxygen
equivalents of carbon lost per nitrate nitrogen that is denitrified. The term Denitr is the
rate of denitrification [gN/L/d]. It will be defined Nitrate Nitrogen.

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Organic Nitrogen (no)

Organic nitrogen increases due to detritus dissolution. It is lost via hydrolysis. The net
gain or loss from the hyporheic sediment zone (Sno,2) is calculated as
S no , 2 rnd DetrDiss 2 ONHydr2

(252)

The hydrolysis rate is calculated as

ONHydr2 k hn (T )n o , 2

(253)

where khn(T) = the temperature-dependent organic nitrogen hydrolysis rate [/d].

Ammonia Nitrogen (na)

Ammonia nitrogen increases due to organic nitrogen hydrolysis and respiration of
phytoplankton and heterotrophic bacteria. It is lost via nitrification and growth of
heterotrophic bacteria. The net gain or loss from the hyporheic sediment zone (Sna,2) is
calculated as
S na , 2 ONHydr2 rna PhytoResp 2 NH4Nitrif 2
rnd [ HeteroResp Pah HeteroGrow]

Ast ,i

(254)

V 2 ,i

The ammonia nitrification rate is computed as

NH4Nitrif 2 Foxna , 2 k na (T ) na , 2

(255)

where kna(T) = the temperature-dependent nitrification rate for ammonia nitrogen [/d] and
Foxna = attenuation due to low oxygen [dimensionless]. Oxygen attenuation is modeled
with the oxygen dependency represented by the parameter Ksona.
The coefficient Pah is the preferences for ammonium as a nitrogen source for
heterotrophic bacteria:
Pah

(k hnxh

na , 2 nn , 2
na , 2 k hnxh

na , 2 )(k hnxh nn , 2 ) (na , 2 nn , 2 )(k hnxh nn , 2 )

(256)

where khnxh = preference coefficient of heterotrophic bacteria for ammonium [mgN/m3].

Nitrate Nitrogen (nn)

84

Nitrate nitrogen increases due to nitrification of ammonia. It is lost via denitrification

and the growth of heterotrophic bacteria. The net gain or loss from the hyporheic
sediment zone (Snn,2) is calculated as
S nn , 2 NH4Nitrif 2 Denitr2 rnd (1 Pah ) HeteroGrow

Ast ,i

(257)

V2,i

The denitrification rate is computed as

Denitr2

c f ,2
0 .1 c f , 2

(1 Foxdn , 2 )k dn (T )nn , 2

(258)

where kdn(T) = the temperature-dependent denitrification rate of nitrate nitrogen [/d] and
Foxdn = effect of low oxygen on denitrification [dimensionless] as modeled by Eqs. (82) to
(84) with the oxygen dependency represented by the parameter Ksodn.

Organic Phosphorus (po)

Dissolved organic phosphorus increases due to dissolution of detritus. It is lost via
hydrolysis. The net gain or loss for the hyporheic sediment zone (Spo,2) is calculated as
S po , 2 rpd DetrDiss 2 OPHydr2

(259)

where
OPHydr2 k hp (T ) po , 2

(260)

where khp(T) = the temperature-dependent organic phosphorus hydrolysis rate [/d].

Inorganic Phosphorus (pi)

Inorganic phosphorus in the hyporheic sediment zone increases due to dissolved organic
phosphorus hydrolysis and respiration of phytoplankton and heterotrophic bacteria. It is
lost via growth of heterotrophic bacteria. The net gain or loss in the hyporheic sediment
zone (Spi,2) is calculated as
S pi , 2 OPHydr2 rpa PhytoResp 2 rpd [HeteroResp HeteroGrow]

Ast ,i
V2 ,i

(261)

Dissolved Oxygen (o)

Dissolved oxygen is lost via oxidation of fast and slow CBOD by suspended bacteria, and
growth and respiration of heterotrophic bacteria. It is also lost due to nitrification,
phytoplankton respiration, and oxidation of non-carbonaceous non-nitrogenous chemical

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oxygen demand (COD). The loss of dissolved oxygen from the hyporheic sediment zone
(So,2) is calculated as
S o , 2 SlowCOxid 2 FastCOxid 2 [ro d HeteroGrow rod HeteroResp]

Ast ,i
V 2 ,i

(262)

ron NH4Nitr2 roa PhytoResp 2 CODoxid 2

The term CODoxid2 is the COD oxidation (mgO2/L/d) as defined in the section below on
the generic constituent.

Pathogen (x)
Pathogens are subject to death in the hyporheic sediment zone. The loss in the hyporheic
zone (Sx,2) is computed as
S x , 2 PathDeath 2

(263)

Pathogen death is due to natural die-off. The death of pathogens in the absence of light is
modeled as a first-order temperature-dependent decay,
PathDeath 2 k dx (T ) x2

(264)

where kdx(T) = temperature-dependent pathogen die-off rate [/d].

Generic constituent (gen)

A generic constituent is available for optional use. The user has the option of either
assuming that the generic constituent has no interaction with other state variables, or it
can be treated as a non-carbonaceous non-nitrogenous chemical oxygen demand (COD).
The generic constituent is also subject to first-order decay and settling in the hyporheic
zone,
S gen , 2 k gen (T ) gen2

(265)

where kgen(T) = temperature-dependent decay rate [/d].

If the generic constituent is used as COD, then the COD oxidation rate (mgO2/L/d) is
determined by
CODoxid 2 k gen (T ) gen

(266)

where gen is in units of mgO2/L.

86

pH
The equilibrium, mass balance, and electroneutrality equations described in the water
column section on pH are used to determine the pH in the hyporheic pore water.

Total Inorganic Carbon (cT)

Total inorganic carbon concentration (cT) increases due to fast carbon oxidation from
suspended bacteria and the growth and respiration of heterotrophic bacteria. It is also
gained due to the respiration of phytoplankton. The net gain in the hyporheic sediment
zone (ScT,2) is calculated as
S cT , 2 rccoSlowCOxid 2 rcco FastCOxid 2
rccd [HeteroGrow HeteroResp]

Ast ,i
V 2 ,i

(267)

rcca PhytoResp 2

The stoichiometric coefficients are derived in the water column section on Total
Inorganic Carbon.

Alkalinity (Alk)
Changes in alkalinity in the hyporheic zone are due to phytoplankton respiration,
heterotrophic bacteria growth and respiration, nitrification, and denitrification. The net
gain or loss for the hyporheic sediment zone (Salk,2) is calculated as
S alk , 2 ralkaa PhytoResp 2
[ ralkda Pah ralkdn (1 Pah ) HeteroGrow ralkda HeteroResp]

Ast ,i
V2 ,i

(268)

ralkn NH4Nitr2 ralkdn Denitr2

where the rs are ratios that translate the processes into the corresponding amount of
alkalinity. The stoichiometric coefficients are derived from in the water column section
on Alkalinity.

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Automatic calibration
Q2K uses a genetic algorithm to determine the optimum values for the kinetic rate
parameters for the model state variables in Table 5. Pelletier et al. (2006) describe the
genetic algorithm in Q2K.
Genetic algorithms are a class of search techniques that can be used to construct
numerical optimization techniques. The genetic algorithm used in Q2K is the public
domain subroutine PIKAIA (Charbonneau and Knapp, 1995). The genetic algorithm finds
the set of selected kinetic rate parameters that maximize the goodness of fit of the model
results compared with measured data. Detailed documentation of the PIKAIA algorithm
is available in Charbonneau and Knapp (1995) and the PIKAIA Web site at the following
link:
http://www.hao.ucar.edu/public/research/si/pikaia/pikaia.html
The genetic algorithm carries out its maximization task on a user-selected number of
model runs to define a population. This population size remains constant throughout the
evolutionary process. Rather than evolving the population until some preset tolerance
criterion is satisfied, the genetic algorithm carries the evolution forward over a userspecified number of generations.

SOD/Nutrient Flux Model

Sediment nutrient fluxes and sediment oxygen demand (SOD) are based on a model
developed by Di Toro (Di Toro et al. 1991, Di Toro and Fitzpatrick. 1993, Di Toro 2001).
The present version also benefited from James Martins (Mississippi State University,
personal communication) efforts to incorporate the Di Toro approach into EPAs WASP
modeling framework.
A schematic of the model is depicted in Figure 22. As can be seen, the approach
allows oxygen and nutrient sediment-water fluxes to be computed based on the
downward flux of particulate organic matter from the overlying water. The sediments are
divided into 2 layers: a thin ( 1 mm) surface aerobic layer underlain by a thicker (10 cm)
lower anaerobic layer. Organic carbon, nitrogen and phosphorus are delivered to the
anaerobic sediments via the settling of particulate organic matter (i.e., phytoplankton and
detritus). There they are transformed by mineralization reactions into dissolved methane,
ammonium and inorganic phosphorus. These constituents are then transported to the
aerobic layer where some of the methane and ammonium are oxidized. The flux of
oxygen from the water required for these oxidations is the sediment oxygen demand. The
following sections provide details on how the model computes this SOD along with the
sediment-water fluxes of carbon, nitrogen and phosphorus that are also generated in the
process.

88

cf o

AEROBIC

WATER

Jpom

CH4

CO2

nn

pi

NH4p

NH4d

NO3

N2

NH4p

NH4d

NO3

N2

PO4p

PO4d

PO4p

PO4d

CH4(gas)

POC
ANAEROBIC

na

PON

POP

DIAGENESIS

METHANE

AMMONIUM

NITRATE

PHOSPHATE

Figure 22 Schematic of SOD-nutrient flux model of the sediments.

Diagenesis
As summarized in Figure 23, the first step in the computation involves determining
how much of the downward flux of particulate organic matter (POM) is converted into
soluble reactive forms in the anaerobic sediments. This process is referred to as
diagenesis. First the total downward flux is computed as the sum of the fluxes of
phytoplankton and detritus settling from the water column
J POM rda v a a p v dt m o

(269)

where JPOM = the downward flux of POM [gD m2 d1], rda = the ratio of dry weight to
chlorophyll a [gD/mgA], va = phytoplankton settling velocity [m/d], ap = phytoplankton
concentration [mgA/m3], vdt = detritus settling velocity [m/d], and mo = detritus
concentration [gD/m3].

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vaap

vdtmo

fG1

rda

JPOC

fG3

roc

JPOM

fG2

rcd
fG1
rnd

JPON

fG2
fG3

rpd
fG1
JPOP

fG2
fG3

JPOC, G1

POC2,G1

JPOC, G2

POC2,G2

JPOC, G3

POC2,G3

JPON, G1

PON2,G1

JPON, G2

PON2,G2

JPON, G3

PON2,G3

JPOP, G1

POP2,G1

JPOP, G2

POP2,G2

JPOP, G3

POP2,G3

JC, G1
JC, G2

JC

JN, G1
JN, G2

JN

JP, G1
JP, G2

JP

Figure 23 Representation of how settling particulate organic particles (phytoplankton and

detritus) are transformed into fluxes of dissolved carbon (JC) , nitrogen (JN) and
phosphorus (JP) in the anaerobic sediments.

Stoichiometric ratios are then used to divide the POM flux into carbon, nitrogen and
phosphorus. Note that for convenience, we will express the particulate organic carbon
(POC) as oxygen equivalents using the stoichiometric coefficient roc. Each of the nutrient
fluxes is further broken down into three reactive fractions: labile (G1), slowly reacting
(G2) and non-reacting (G3).
These fluxes are then entered into mass balances to compute the concentration of
each fraction in the anaerobic layer. For example, for labile POC, a mass balance is
written as
H2

dPOC 2,G1
dt

T 20
J POC ,G1 k POC ,G1 POC
,G1 H 2 POC 2 ,G1 w2 POC 2 ,G1

(270)

where H2 = the thickness of the anaerobic layer [m], POC2,G1 = the concentration of the
labile fraction of POC in the anaerobic layer [gO2/m3], JPOC,G1 = the flux of labile POC
delivered to the anaerobic layer [gO2/m2/d], kPOC,G1 = the mineralization rate of labile POC
[d1], POC,G1 = temperature correction factor for labile POC mineralization
[dimensionless], and w2 = the burial velocity [m/d]. At steady state, Eq. 191 can be solved
for
POC 2,G1

J POC ,G1
T 20
k POC ,G1 POC
,G1 H 2 v b

(271)

90

The flux of labile dissolved carbon, JC,G1 [gO2/m2/d], can then be computed as
T 20
J C ,G1 k POC ,G1 POC
,G1 H 2 POC 2 ,G1

(272)

In a similar fashion, a mass balance can be written and solved for the slowly reacting
dissolved organic carbon. This result is then added to Eq. 193 to arrive at the total flux of
dissolved carbon generated in the anaerobic sediments.
J C J C ,G1 J C ,G 2

(273)

Similar equations are developed to compute the diagenesis fluxes of nitrogen, JN

[gN/m2/d], and phosphorus JP [gP/m2/d].

Ammonium
Based on the mechanisms depicted in Figure 22, mass balances can be written for total
ammonium in the aerobic layer and the anaerobic layers,

H1

dNH 4,1
dt

12 f pa 2 NH 4, 2 f pa1 NH 4,1 K L12 f da 2 NH 4, 2 f da1 NH 4,1 w2 NH 4,1

K NH 4
o
na
NH 4,1 T 20
s
f da1 NH 4,1
NH 4
f da1 NH 4,1
s
K NH 4 NH 4,1 2 K NH 4,O 2 o
1000

(274)

H2

dNH 4, 2
dt

J N 12 f pa1 NH 4,1 f pa 2 NH 4, 2 K L12 f da1 NH 4,1 f da 2 NH 4, 2

w2 NH 4,1 NH 4, 2

(275)

where H1 = the thickness of the aerobic layer [m], NH4,1 and NH4,2 = the concentration of
total ammonium in the aerobic layer and the anaerobic layers, respectively [gN/m3], na =
the ammonium concentration in the overlying water [mgN/m3], NH4,1 = the reaction
velocity for nitrification in the aerobic sediments [m/d], NH4 = temperature correction
factor for nitrification [dimensionless], KNH4 = ammonium half-saturation constant
[gN/m3], o = the dissolved oxygen concentration in the overlying water [gO2/m3], and
KNH4,O2 = oxygen half-saturation constant [mgO2/L], and JN = the diagenesis flux of
ammonium [gN/m2/d].
The fraction of ammonium in dissolved (fdai) and particulate (fpai) form are computed
as

QUAL2K

91

July 16, 2004

f dai

1
1 mi ai

(276)

f pai 1 f dai

(277)

where mi = the solids concentration in layer i [gD/m3], and ai = the partition coefficient
for ammonium in layer i [m3/gD].
The mass transfer coefficient for particle mixing due to bioturbation between the
layers, 12 [m/d], is computed as
12

T 20
D p Dp
POC 2,G1 / roc

H2

POC R

o
K M , Dp o

(278)

where Dp = diffusion coefficient for bioturbation [m2/d], Dp = temperature coefficient

[dimensionless], POCR = reference G1 concentration for bioturbation [gC/m3] and KM,Dp =
oxygen half-saturation constant for bioturbation [gO2/m3].
The mass transfer coefficient for pore water diffusion between the layers, KL12 [m/d],
is computed as,
K L12

T 20
D d Dd
H2 / 2

(279)

where Dd = pore water diffusion coefficient [m2/d], and Dd = temperature coefficient

[dimensionless].
The mass transfer coefficient between the water and the aerobic sediments, s [m/d], is
computed as
s

SOD
o

(280)

where SOD = the sediment oxygen demand [gO2/m2/d].

At steady state, Eqs. 195 and 196 are two simultaneous nonlinear algebraic equations.
The equations can be linearized by assuming that the NH4,1 term in the Monod term for
nitrification is constant. The simultaneous linear equations can then be solved for NH4,1
and NH4,2. The flux of ammonium to the overlying water can then be computed as
n

J NH 4 s f da1 NH 4,1 a
1000

(281)

92

Nitrate
Mass balances for nitrate can be written for the aerobic and anaerobic layers as
H1

dNO3,1
dt

nn

NO3,1
1000

2
NO
o
3,1 T 20
f da1 NH 4,1
NO 3 NO3,1
2 K NH 4,O 2 o
s

K L12 NO3, 2 NO3,1 w2 NO3,1 s

2
NH
4 ,1

T 20
NH
4

K NH 4
K NH 4 NH 4,1

(282)

H2

dNO3, 2
dt

T 20
J N K L12 NO3,1 NO3, 2 w2 NO3,1 NO3, 2 NO 3, 2 NO
3 NO3, 2

(283)

where NO3,1 and NO3,2 = the concentration of nitrate in the aerobic layer and the anaerobic
layers, respectively [gN/m3], nn = the nitrate concentration in the overlying water
[mgN/m3], NO3,1 and NO3,2 = the reaction velocities for denitrification in the aerobic and
anaerobic sediments, respectively [m/d], and NO3 = temperature correction factor for
denitrification [dimensionless].
In the same fashion as for Eqs. 195 and 196, Eqs. 203 and 204 can be linearized and
solved for NO3,1 and NO3,2. The flux of nitrate to the overlying water can then be
computed as
n

J NO 3 s NO3,1 n
1000

(284)

Denitrification requires a carbon source as represented by the following chemical

equation,
5CH 2 O 4NO 3 4H 5CO 2 2N 2 7H 2 O

(285)

The carbon requirement (expressed in oxygen equivalents per nitrogen) can therefore be
computed as
rondn 2.67

gO 2 5 moleC 12 gC/moleC
gO 2
1 gN

0.00286
gC 4 moleN 14 gN/moleN 1000 mgN
mgN

(286)

Therefore, the oxygen equivalents consumed during denitrification, JO2,dn [gO2/m2/d], can
be computed as
J O 2, dn 1000

QUAL2K

2
NO

mgN
3,1
T 20
T 20

rondn
NO
3 NO3,1 NO 3, 2 NO 3 NO3, 2

gN
s

93

(287)

July 16, 2004

Methane
The dissolved carbon generated by diagenesis is converted to methane in the anaerobic
sediments. Because methane is relatively insoluble, its saturation can be exceeded and
methane gas produced. As a consequence, rather than write a mass balance for methane in
the anaerobic layer, an analytical model developed by Di Toro et al. (1990) is used to
determine the steady-state flux of dissolved methane corrected for gas loss delivered to
the aerobic sediments.
First, the carbon diagenesis flux is corrected for the oxygen equivalents consumed
during denitrification,
J CH 4,T J C J O 2, dn

(288)

where JCH4,T = the carbon diagenesis flux corrected for denitrification [gO2/m2/d]. In other
words, this is the total anaerobic methane production flux expressed in oxygen
equivalents.
If JCH4,T is sufficiently large ( 2KL12Cs), methane gas will form. In such cases, the flux
can be corrected for the gas loss,
J CH 4,d

(289)

2 K L12 C s J CH 4 ,T

where JCH4,d = the flux of dissolved methane (expressed in oxygen equivalents) that is
generated in the anaerobic sediments and delivered to the aerobic sediments [gO2/m2/d],
Cs = the saturation concentration of methane expressed in oxygen equivalents [mgO2/L].
If JCH4,T < 2KL12Cs, then no gas forms and
J CH 4, d J CH 4,T

(290)

The methane saturation concentration is computed as

H

20 T
C s 100 1
1.024
10

(291)

where H = water depth [m] and T = water temperature [oC].

A methane mass balance can then be written for the aerobic layer as
H1

dCH 4,1
dt

J CH 4, d s c f CH 4,1

2
CH
4 ,1

T 20
CH
4 CH 4,1

(292)

where CH4,1 = methane concentration in the aerobic layer [gO2/m3], cf = fast CBOD in the
overlying water [gO2/m3], CH4,1 = the reaction velocity for methane oxidation in the

94

aerobic sediments [m/d], and CH4 = temperature correction factor [dimensionless]. At

steady, state, this balance can be solved for
J CH 4, d sc f

CH 4,1

2
CH
4 ,1

(293)

T 20
CH
4

The flux of methane to the overlying water, JCH4 [gO2/m2/d], can then be computed as

J CH 4 s CH 4,1 c f

(294)

SOD
The SOD [gO2/m2/d] is equal to the sum of the oxygen consumed in methane oxidation
and nitrification,
SOD CSOD NSOD

(295)

where CSOD = the amount of oxygen demand generated by methane oxidation

[gO2/m2/d] and NSOD = the amount of oxygen demand generated by nitrification
[gO2/m2/d]. These are computed as
CSOD

2
CH
4 ,1

NSOD ron

T 20
CH
4 CH 4 ,1

2
NH
4,1

T 20
NH
4

(296)

K NH 4
o
f da1 NH 4,1
K NH 4 NH 4,1 2 K NH 4,O 2 o

(297)

where ron = the ratio of oxygen to nitrogen consumed during nitrification [= 4.57
gO2/gN].

Inorganic Phosphorus
Mass balances can be written total inorganic phosphorus in the aerobic layer and the
anaerobic layers as

H1

dPO4,1
dt

12 f pp 2 PO4, 2 f pp1 PO4,1 K L12 f dp 2 PO4, 2 f dp1 PO4,1

w2 PO4,1

QUAL2K

95

pi

s
f da1 PO4,1
1000

(298)

July 16, 2004

H2

dPO4, 2
dt

J P 12 f pp1 PO4,1 f pp 2 PO4, 2 K L12 f dp1 PO4,1 f dp 2 PO4, 2

w2 PO4,1 PO4, 2

(299)

where PO4,1 and PO4,2 = the concentration of total inorganic phosphorus in the aerobic
layer and the anaerobic layers, respectively [gP/m3], pi = the inorganic phosphorus in the
overlying water [mgP/m3], and JP = the diagenesis flux of phosphorus [gP/m2/d].
The fraction of phosphorus in dissolved (fdpi) and particulate (fppi) form are computed
as
f dpi

1
1 mi pi

f ppi 1 f dpi

(300)

(301)

where pi = the partition coefficient for inorganic phosphorus in layer i [m3/gD].

The partition coefficient in the anaerobic layer is set to an input value. For the aerobic
layer, if the oxygen concentration in the overlying water column exceeds a critical
concentration, ocrit [gO2/m3], then the partition coefficient is increased to represent the
sorption of phosphorus onto iron oxyhydroxides as in
p1 p 2 PO 4,1

(302)

where PO4,1 is a factor that increases the aerobic layer partition coefficient relative to
the anaerobic coefficient.
If the oxygen concentration falls below ocrit then the partition coefficient is decreased
smoothly until it reaches the anaerobic value at zero oxygen,
p1 p 2 PO 4,1 o / ocrit

(303)

Equations 219 and 220 can be solved for PO4,1 and PO4,2. The flux of phosphorus to
the overlying water can then be computed as
p

J PO 4 s PO4,1 i
1000

(304)

Solution Scheme

96

Although the foregoing sequence of equations can be solved, a single computation will
not yield a correct result because of the interdependence of the equations. For example,
the surface mass transfer coefficient s depends on SOD. The SOD in turn depends on the
ammonium and methane concentrations which themselves are computed via mass
balances that depend on s. Hence, an iterative technique must be used. The procedure
used in QUAL2K is
1. Determine the diagenesis fluxes: JC, JN and JP.
2. Start with an initial estimate of SOD,
SODinit J C ron' J N

(305)

where ron = the ratio of oxygen to nitrogen consumed for total conversion of
ammonium to nitrogen gas via nitrification/denitrification [= 1.714 gO2/gN]. This
ratio accounts for the carbon utilized for denitrification.
3. Compute s using
s

SODinit
o

(306)

4. Solve for ammonium, nitrate and methane, and compute the CSOD and NSOD.
5. Make a revised estimate of SOD using the following weighted average
SOD

SODinit CSOD NSOD

2

(307)

6. Check convergence by calculating an approximate relative error

a

SOD SODinit
100%
SOD

(308)

7. If a is greater than a prespecified stopping criterion s then set SODinit = SOD and
return to step 2.
8. If convergence is adequate (a s), then compute the inorganic phosphorus
concentrations.
9. Compute the ammonium, nitrate, methane and phosphate fluxes.

Supplementary Fluxes

QUAL2K

97

July 16, 2004

Because of the presence of organic matter deposited prior to the summer steady-state
period (e.g., during spring runoff), it is possible that the downward flux of particulate
organic matter is insufficient to generate the observed SOD. In such cases, a
supplementary SOD can be prescribed,
SODt SOD SOD s

(309)

where SODt = the total sediment oxygen demand [gO2/m2/d], and SODs = the
supplementary SOD [gO2/m2/d]. In addition, prescribed ammonia and methane fluxes can
be used to supplement the computed fluxes.

98

REFERENCES
Adams, E.E., D. J. Cosler, and K.R. Helfrich. 1987. "Analysis of evaporation data from
heated ponds", cs-5171, research project 2385-1, Electric Power Research Institute,
Palo Alto, California 94304. April.
Andrews and Rodvey, 1980. Heat exchange between water and tidal flats. D.G.M 24(2).
(in German)
Asaeda, T., and T. Van Bon, Modelling the effects of macrophytes on algal blooming in
eutrophic shallow lakes. Ecol Model 104: 261-287, 1997.
Baly, E.C.C. 1935. The Kinetics of Photosynthesis. Proc. Royal Soc. London Ser. B,
117:218-239.
Banks, R. B. 1975. "Some Features of Wind Action on Shallow Lakes." J. Environ Engr.
Div. ASCE. 101(EE5): 813-827.
Banks, R. B. and Herrera, F. F. 1977. "Effect of Wind and Rain on Surface Reaeration."
J. Environ Engr. Div. ASCE. 103(EE3): 489-504.
Barnwell, T.O., Brown, L.C., and Mareck, W. 1989). Application of Expert Systems
Technology in Water Quality Modeling. Water Sci. Tech. 21(8-9):1045-1056.
Bejan, A. 1993. Heat Transfer. Wiley, New York, NY.
Bencala, K.E. and R.A. Walters. 1983. Simulation of solute transport in a mountain
pool-and-riffle stream: a transient storage model. Water Resources Research 19:718724.
Bowie, G.L., Mills, W.B., Porcella, D.B., Campbell, C.L., Pagenkopf, J.R., Rupp, G.L.,
Johnson, K.M., Chan, P.W.H., Gherini, S.A. and Chamberlin, C.E. 1985. Rates,
Constants, and Kinetic Formulations in Surface Water Quality Modeling. U.S. Envir.
Prot. Agency, ORD, Athens, GA, ERL, EPA/600/3-85/040.
Brady, D.K., Graves, W.L., and Geyer, J.C. 1969. Surface Heat Exchange at Power Plant
Cooling Lakes, Cooling Water Discharge Project Report, No. 5, Edison Electric Inst.
Pub. No. 69-901, New York, NY.
Bras, R.L. 1990. Hydrology. Addison-Wesley, Reading, MA.
Brown, L.C., and Barnwell, T.O. 1987. The Enhanced Stream Water Quality Models
QUAL2E and QUAL2E-UNCAS, EPA/600/3-87-007, U.S. Environmental Protection
Agency, Athens, GA, 189 pp.
Brunt, D. 1932. Notes on radiation in the atmosphere: I. Quart J Royal Meteorol Soc
58:389-420.
Brutsaert, W. 1982. Evaporation into the atmosphere: theory, history, and applications.
D.Reidel Publishing Co., Hingham MA, 299 p.
Butts, T. A. and Evans, R. L. 1983. Effects of Channel Dams on Dissolved Oxygen
Concentrations in Northeastern Illinois Streams, Circular 132, State of Illinois, Dept.
of Reg. and Educ., Illinois Water Survey, Urbana, IL.
Carslaw, H.S. and Jaeger, J.C. 1959. Conduction of Heat in Solids, Oxford Press, Oxford,
UK, 510 pp.
Cengel, Y.A. 1998 Heat Transfer: A Practical Approach. New York, McGraw-Hill.
Chapra and Canale 2002. Numerical Methods for Engineers, 4th Ed. New York, McGrawHill.
Chapra, S.C. 1997. Surface water quality modeling. New York, McGraw-Hill.

Chow, V.T., Maidment, D.R., and Mays, L.W. 1988. Applied Hydrology. New York,
McGraw-Hill, 592 pp.
Chapra, S.C. 1997. Surface Water Quality Modeling. McGraw-Hill, New York.
Chapra S.C. and R.P. Canale. 2002. Numerical Methods for Engineers. McGraw-Hill,
New York.
Chapra, S.C. and G.J. Pelletier. 2003. QUAL2K: A Modeling Framework for Simulating
River and Stream Water Quality (Beta Version): Documentation and Users Manual.
Civil and Environmental Engineering Dept., Tufts University, Medford,
MA.Churchill, M.A., Elmore, H.L., and Buckingham, R.A. 1962. The prediction of
stream reaeration rates. J. Sanit. Engrg. Div. , ASCE, 88{4),1-46.
Charbonneau, P., and Knapp, B. 1995, A User's guide to PIKAIA 1.0, NCAR Technical
Note 418+IA (Boulder: National Center for Atmospheric Research).
(http://www.hao.ucar.edu/public/research/si/pikaia/pikaia.html)
Coffaro, G. and A. Sfriso, Simulation model of Ulva rigida growth in shallow water of
the Lagoon of Venice. Ecol Model, 102: 55-66, 1997.
Covar, A. P. 1976. "Selecting the Proper Reaeration Coefficient for Use in Water Quality
Models." Presented at the U.S. EPA Conference on Environmental Simulation and
Modeling, April 19-22, 1976, Cincinnati, OH.
Crawford, T.M. and C.E. Duchon. 1999. An improved parameterization for estimating
effective atmospheric emissivity for use in calculating daytime downwelling
longwave radiation. J.Appl.Meteorol. 38, 474-480.
Culf, A.D. and J.H.C. Gash. 1993. Longwave radiation from clear skies in Niger: a
comparison of observations with simple formulas. J.Appl.Meteorol. 32, 539-547.
Di Toro, D. M. and J. F. Fitzpatrick. 1993. Chesapeake Bay sediment flux model. Tech.
Report EL-93-2, U.S. Army Corps of Engineers, Waterways Experiment Station,
Vicksburg, Mississippi, 316 pp.
Di Toro, D.M, Paquin, P.R., Subburamu, K. and Gruber, D.A. 1991. Sediment Oxygen
Demand Model: Methane and Ammonia Oxidation. J. Environ. Eng., 116(5):945-986.
Di Toro, D.M. 1978. Optics of Turbid Estuarine Waters: Approximations and
Applications. Water Res. 12:1059-1068.
Di Toro, D.M. 2001. Sediment Flux Modeling. Wiley-Interscience, New York, NY.
Droop, M.R. 1974. The nutrient status of algal cells in continuous culture.
J.Mar.Biol.Assoc. UK 54:825-855.
Ecology. 2003. Shade.xls - a tool for estimating shade from riparian vegetation.
Washington State Department of Ecology.
http://www.ecy.wa.gov/programs/eap/models/
Edinger, J.E., Brady, D.K., and Geyer, J.C. 1974. Heat Exchange and Transport in the
Environment. Report No. 14, EPRI Pub. No. EA-74-049-00-3, Electric Power
Research Institute, Palo Alto, CA.
Fernald, A.G. P.J. Wiginton, and D.H. Landers. 2001. Transient storage and hyporheic
flow along the Willamette River, Oregon: field measurements and model estimates.
Water Resources Research 37(6):1681-1694.
Finnemore, E.J. and Franzini, J.B. 2002. Fluid Mechanics with Engineering Applications,
10th Ed. New York, McGraw, Hill.
Geiger, R. 1965. The climate near the ground. Harvard University Press. Cambridge,
MA.

100

Gooseff, M.N., S.M. Wondzell, R. Haggerty, and J. Anderson. 2003. in press. Advances
in Water Resources, special issue on hyporheic zone modeling.
(cc.usu.edu/~gooseff/web_cv/ gooseff_etal_AWR_paper_color.PDF)
Gordon, N.D, T.A. McMahon, and B.L. Finlayson. 1992. Stream Hydrology, An
Introduction for Ecologists. Published by John Wiley and Sons.
Grigull, U. and Sandner, H. 1984. Heat Conduction. Springer-Verlag, New York, NY.
Grimm, N.B., and S.G. Fisher. 1984. Exchange between interstitial and surface water:
implications for stream metabolism and nutrient cycling. Hydrobiologia 111:219228.
Hamilton, D.P., and S.G. Schladow, Prediction of water quality in lakes and reservoirs. 1.
Model description. Ecol Model, 96: 91-110, 1997.
Harbeck, G. E., 1962, A practical field technique for measuring reservoir evaporation
utilizing mass-transfer theory. US Geological Survey Professional Paper 272-E, 1015.
Harned, H.S., and Hamer, W.J. 1933. The Ionization Constant of Water. J. Am., Chem.
Soc. 51:2194.
Hart, D.R. 1995. Parameter estimate and stochastic interpretation of the transient storage
model for solute transport in streams. Water Resources Research 31:323-328.
Harvey, J.W. and B.J. Wagner. 2000. Quantifying hydrologic interactions between
streams and their subsurface hyporheic zones. In: Streams and Groundwaters. Edited
by J.B. Jones and P.J. Mulholland. Academic Press.
Hatfield, J.L., R.J. Reginato, and S.B. Idso. 1983. Comparison of longwave radiation
calculation methods over the United States. Water Resources Research, 19 (1) 285288.
Helfrich, K.R., E.E. Adams, A.L. Godbey, and D.R.F. Harleman. 1982. Evaluation of
models for predicting evaporative water loss in cooling impoundments. Report CS2325, Research project 1260-17. Electric Power Research Institute, Pala Alto, CA.
March 1982.
Hellweger, F/L., K.L. Farley, U. Lall, and D.M. DiToro. 2003. Greedy algae reduce
arsenate. Limnol.Oceanogr. 48(6), 2003, 2275-2288.
Hutchinson, G.E. 1957. A Treatise on Limnology, Vol. 1, Physics and Chemistry. Wiley,
New York, NY.
Idso, S.B. 1981. A set of equations for full spectrum and 8-14 m and 10.5-12.5 m
thermal radiation from cloudless skies. Water Resources Research, 17, 295-304.
Idso, S.B. and R.D. Jackson. 1969. Thermal radiation from the atmosphere.
J.Geophys.Res., 74, 3397-5403.
Ikusima, I. (1970). Ecological studies on the productivity of aquatic plant communities
IV: Light conditions and community photosynthetic prodcution. Bot. Mag. Tokyo,
83, 330-341.
Jobson, H.E. 1977. Bed Conduction Computation for Thermal Models. J. Hydraul. Div.
ASCE. 103(10):1213-1217.
Kasahara, T. and S.M. Wondzell. 2003. Geomorphic controls on hyporheic exchange
flow in mountain streams. Water Resources Research 39(1)1005.
Koberg, G.E. 1964. Methods to compute long-wave radiation from the atmosphere and
reflected solar radiation from a water surface. US Geological Survey Professional
Paper 272-F.

QUAL2K

101

July 16, 2004

Kreith, F. and Bohn, M.S. 1986. Principles of Heat Transfer, 4th Ed. Harper and Row,
New York, NY.
Laws, E. A. and Chalup, M. S. 1990. A Microalgal Growth Model. Limnol. Oceanogr.
35(3):597-608.
Leichtfried, M. 1988. Bacterial substrates in gravel beds of a second order alpine stream
(Project Ritrodat-Lunz, Austria). Verh. Internat. Verein. Limnol. 23:1325-1332.
Leichtfried, M. 1991. POM in bed sediments of a gravel stream (Ritrodat-Lunz Study
area, Austria). Verh. Internat. Verein. Limnol. 24:1921-1925.
LI-COR, 2003. Radiation Measurement Instruments, LI-COR, Lincoln, NE, 30 pp.
Likens, G. E., and Johnson, N. M. (1969). "Measurements and analysis of the annual heat
budget for sediments of two Wisconsin lakes." Limnol. Oceanogr., 14(1):115-135.
Mackay, D. and Yeun, A.T.K. 1983. Mass Transfer Coefficient Correlations for
Volatilization of Organic Solutes from Water. Environ. Sci. Technol. 17:211-233.
Marciano, J.K. and G.E. Harbeck. 1952. Mass transfer studies in water loss investigation:
Lake Hefner studies. Geological Circular 229. U.S. Geological Survey, Washington
DC.
Meeus, J. 1999. Astronomical algorithms. Second edition. Willmann-Bell, Inc.
Richmond, VA.
Melching, C.S. and Flores, H.E. 1999. Reaeration Equations from U.S. Geological
Survey Database. J. Environ. Engin., 125(5):407-414.
Mills, A.F. 1992. Heat Transfer. Irwin, Homewood, IL.
Moog, D.B., and Iirka, G.H. 1998. Analysis of reaeration equations using mean
multiplicative error. J. Environ. Engrg., ASCE, 124(2), 104-110.
Mulholland, P.J., E.R. Marzolf, J.R. Webster, D.R. Hart, and S.P. Hendricks. 1997.
Evidence that hyporheic zones increase heterotrophic metabolism and phosphorus
uptake in forest streams. Limnol. Ocean. 42(3):443-451.
Naegili, M.W., and U. Uehlinger. 1997. Contribution of the hyporheic zone to
ecosystem metabolism in a prealpine gravel-bed river. J. N. Am. Benthol. Soc.
16(4):794-804.
Nakshabandi, G.A. and H. Kohnke. 1965. Thermal conductivity and diffusivity of soils as
related to moisture tension and other physical properties. Agr. Met. Vol 2.
O'Connor, D.J., and Dobbins, W.E. 1958. Mechanism of reaeration in natural streams.
Trans. ASCE, 123, 641-684.
Owens, M., Edwards, R.W., and Gibbs, J.W. 1964. Some reaeration studies in streams.
Int. J. Air and Water Pollution, 8, 469-486.
Pelletier, G.J., S.C. Chapra, and H.Tao. QUAL2Kw a framework for modeling water
quality in streams and rivers using a genetic algorithm for calibration. Environmental
Modelling and Software. 21(2006):419-425.
Plummer, L.N. and Busenberg, E. 1982. The Solubilities of Calcite, Aragonite and
Vaterite in CO2-H2O Solutions Between 0 and 90 oC, and an Evaluation of the
Aqueous Model for the System CaCO3CO2H2O. Geochim. Cosmochim. 46:10111040.
Poole, G.C., and C. Berman. 2001. An ecological perspective on in-stream temperature:
natural heat dynamics and mechanisms of human-caused thermal degradation.
Environmental Management 27(6):787-802.
Raudkivi, A. I. 1979. Hydrology. Pergamon, Oxford, England.

102

Redfield, A.C., Ketchum, B.H. and Richards, F.A. 1963. The Influence of Organisms on
the Composition of Seawater, in The Sea, M.N. Hill, ed. Vol. 2, pp. 27-46, WileyInterscience, NY.
Riley, G.A. 1956. Oceanography of Long Island Sound 1952-1954. II. Physical
Oceanography, Bull. Bingham Oceanog. Collection 15, pp. 15-16.
Rosgen, D. 1996. Applied river morphology. Wildland Hydrology publishers. Pagosa
Springs, CO.
Rutherford, J.C., S. Blackett, C. Blackett, L. Saito, and R.J Davies-Colley. 1997.
Predicting the effects of shade on water temperature in small streams. New Zealand
Journal of Marine and Freshwater Research, 1997, Vol. 31:707-721.
Rutherford, J.C., Scarsbrook, M.R. and Broekhuizen, N. 2000. Grazer Control of Stream
Algae: Modeling Temperature and Flood Effects. J. Environ. Eng. 126(4):331-339.
Ryan, P.J. and D.R.F. Harleman. 1971. Prediction of the annual cycle of temperature
changes in a stratified lake or reservoir. Mathematical model and users manual.
Ralph M. Parsons Laboratory Report No. 137. Massachusetts Institute of Technology.
Cambridge, MA.
Ryan, P.J. and K.D. Stolzenbach.1972. Engineering aspects of heat disposal from power
generation, (D.R.F. Harleman, ed.). R.M. Parson Laboratory for Water Resources and
Hydrodynamics, Department of Civil Engineering, Massachusetts Institute of
Technology, Cambridge, MA
Shanahan, P. 1984. Water temperature modeling: a practical guide. In: Proceedings of
stormwater and water quality model users group meeting, April 12-13, 1984. USEPA,
EPA-600/9-85-003. (users.rcn.com/shanahan.ma.ultranet/TempModeling.pdf).
Smith, E.L. 1936. Photosynthesis in Relation to Light and Carbon Dioxide. Proc. Natl.
Acad. Sci. 22:504-511.
Spacil, R. and M. Rulik. 1998. Measurements of proteins in the hyporheic zone of Sitka
Stream, Czech Republic. Acta Univ. Palack. Olomuc. Fac. Rerum. Naturalium.
36:75-81.
Sridhar, V., and R.L. Elliott. 2002. On the development of a simple downwelling
longwave radiation scheme. Agriculture and Forest Meteorology, 112 (2002) 237-243.
Steele, J.H. 1962. Environmental Control of Photosynthesis in the Sea. Limnol.
Oceanogr. 7:137-150.
Stumm, W. and Morgan, J.J. 1996. Aquatic Chemistry, New York, Wiley-Interscience,
1022 pp.
Thackston, E. L., and Dawson, J.W. III. 2001. Recalibration of a Reaeration Equation. J.
Environ. Engrg., 127(4):317-320.
Thackston, E. L., and Krenkel, P. A. 1969. Reaeration-prediction in natural streams. J.
Sanit. Engrg. Div., ASCE, 95(1), 65-94.
Titus, J. E. and M. S. Adams (1979). Coexistence and the comparitive light relations of
the submerged macrophytes Myriophyllum spicatum L. and Vallisneria americana
Michx. Oecologia, 40, 273-286.
Tsivoglou, E. C., and Neal, L.A. 1976. Tracer Measurement of Reaeration. III. Predicting
the Reaeration Capacity of Inland Streams. Journal of the Water Pollution Control
Federation, 48(12):2669-2689.
Thomann, R.V. and Mueller, J.A. 1987. Principles of Surface Water Quality Modeling
and Control. New York, Harper-Collins.

QUAL2K

103

July 16, 2004

TVA, 1972. Heat and mass transfer between a water surface and the atmosphere. Water
Resources Research, Laboratory Report No. 14. Engineering Laboratory, Division of
Water Control Planning, Tennessee Valley Authority, Norris TN.
Van der Bijl, L., K. Sand-Jensen, and A. L. Hjermind (1989). Photosynthesis and canopy
structure of a submerged plan, Potamogeton pectinatus, in a Danish lowland stream.
Journal of Ecology, 77, 947-962.
Wanninkhof, R., Ledwell, I. R., and Crusius, I. 1991. "Gas Transfer Velocities on Lakes
Measured with Sulfur Hexafluoride." In Symposium Volume of the Second
International Conference on Gas Transfer at Water Surfaces, S.C. Wilhelms and I.S.
Gulliver, eds., Minneapolis, MN .
Wood, K.G. 1974. Carbon Dioxide Diffusivity Across the Air-Water Interface. Archiv fr
Hydrobiol. 73(1):57-69.

104

APPENDIX A: NOMENCLATURE
Symbol
Aacres ,i

[CO2]s
[CO32]
[H+]
[H2CO3*]
[HCO3]
[OH]
a
a"
a
a1
Aa
Ab
ab
Ac
ad
Alk
ap
ap
at
atc
B
b
B0
bd
c1
cf
cf
Cgb(T)
CH4,1
CL
cnps,i,j
Cp
cps,i,j
cs

Definition
surface area of reach i
saturation concentration of carbon dioxide
carbonate ion
hydronium ion
sum of dissolved carbon dioxide and carbonic acid
bicarbonate ion
hydroxyl ion
velocity rating curve coefficient
mean atmospheric transmission coefficient after
scattering and absorption
mean atmospheric transmission coefficient
atmospheric molecular scattering coefficient for
radiation transmission
atmospheric long-wave radiation coefficient
atmospheric long-wave radiation coefficient
bottom algae
cross-sectional area
coefficient correcting dam reaeration for water
quality
alkalinity
phytoplankton
phytoplankton concentration
atmospheric attenuation
atmospheric transmission coefficient
average reach width
velocity rating curve exponent
bottom width
coefficient correcting dam reaeration for dam type
Bowen's coefficient
fast reacting CBOD
fast CBOD in the overlying water
temperature-dependent maximum photosynthesis
rate
methane concentration in the aerobic sediment layer
fraction of sky covered with clouds
jth non-point source concentration for reach i
specific heat of water
jth point source concentration for reach i
slowly reacting CBOD

Units
acres
mole/L
mole/L
mole/L
mole/L
mole/L
mole/L
dimensionless
dimensionless
dimensionless
dimensionless
dimensionless
mmHg-0.5 or mb-0.5
gD/m2
m2
dimensionless
eq L1 or
mgCaCO3/L
mgC/L
mgA/m3
dimensionless
dimensionless
m
dimensionless
m
dimensionless
0.47 mmHg/oC
mgO2/L
gO2/m3
gD/(m2 d)
gO2/m3
dimensionless
o
C
cal/(g oC)
o
C
mgO2/L

Cs
CSOD
cT
c'T,i1
d
Dd
Dp
Ei
eair
elev
En
Ep,i
eqtime
es
f
fdai
fdpi
FLp
Foxcf
Foxdn
Foxna
Foxrb
Foxrp
fpai
fppi
Fu
g
gX
H
H
Hd
Hi
Hsed
I(0)
I0

saturation concentration of methane

the amount of oxygen demand generated by
methane oxidation
total inorganic carbon
concentration of inorganic carbon entering reach
below a dam
dust attenuation coefficient
pore water diffusion coefficient
diffusion coefficient for bioturbation
bulk dispersion coefficient between reaches i and i +
1
air vapor pressure
elevation above sea level
numerical dispersion
longitudinal dispersion between reaches i and i + 1
equation of time: the difference between mean solar
time and true solar time when located on the
reference longitude of the time zone considered
saturation vapor pressure at water surface
photoperiod
fraction of ammonium in dissolved form in sediment
layer i
fraction of inorganic phosphorus in dissolved form
in sediment layer i
phytoplankton growth attenuation due to light
attenuation of CBOD oxidation due to low oxygen
enhancement of denitrification at low oxygen
concentration
attenuation due to low oxygen
attenuation due to low oxygen
attenuation due to low oxygen
fraction of ammonium in particulate form in
sediment layer i
fraction of inorganic phosphorus in particulate form
in sediment layer i
fraction unionized ammonia
acceleration due to gravity
mass of element X
water depth
water depth
drop in water elevation for a dam
thickness of sediment layer i
sediment thickness
solar radiation at water surface
extraterrestrial radiation

mgO2/L
gO2/m2/d
mole L1
mgO2/L
dimensionless
m2/d
m2/d
m3/d
mm Hg
m
m2/d
m2/s
minutes
mmHg
fraction of day
dimensionless
dimensionless
dimensionless
dimensionless
dimensionless
dimensionless
dimensionless
dimensionless
dimensionless
dimensionless
= 9.81 m/s2
g
m
m
m
m
cm
cal/cm2/d
cal/cm2/d
106

Jan
Jbr
Jc
JC,G1
JCH4
JCH4,d
JCH4,T
Je
Jh
JN
JO2,dn
JP
JPOC,G1
JPOM
Jsi
Jsn
k(T)
K1
K2
Ka
ka(T)
kac(T)
kdb(T)
kdc(T)
kdn(T)
kdp(T)
kdt(T)
kdx(T)
ke
keb
kgp(T)
KH
khc(T)
khn(T)
khnxb
khnxp
QUAL2K

net atmospheric longwave radiation flux

longwave back radiation flux from water
conduction flux
flux of labile dissolved carbon
Flux of methane from sediments to the overlying
water
flux of dissolved methane generated in anaerobic
sediments corrected for methane gas formation
carbon diagenesis flux corrected for denitrification
evaporation flux
air-water heat flux
nitrogen diagenesis flux
oxygen equivalents consumed during denitrification
phosphorus diagenesis flux
the flux of labile POC delivered to the anaerobic
sediment layer
the downward flux of POM
sediment-water heat flux
net solar shortwave radiation flux
temperature dependent first-order reaction rate
acidity constant for dissociation of carbonic acid
acidity constant for dissociation of bicarbonate
equilibrium coefficient for ammonium dissociation
temperature-dependent oxygen reaeration
coefficient
temperature-dependent carbon dioxide reaeration
coefficient
temperature-dependent bottom algae death rate
temperature-dependent fast CBOD oxidation rate
temperature-dependent denitrification rate
temperature-dependent phytoplankton death rate
temperature-dependent detritus dissolution rate
temperature-dependent pathogen die-off rate
light extinction coefficient
a background coefficient accounting for extinction
due to water and color
maximum photosynthesis rate at temperature T
Henry's constant
temperature-dependent slow CBOD hydrolysis rate
temperature-dependent organic nitrogen hydrolysis
rate
preference coefficient of bottom algae for
ammonium
preference coefficient of phytoplankton for
107

cal/(cm2 d)
cal/(cm2 d)
cal/(cm2 d)
gO2/m2/d
gO2/m2/d
gO2/m2/d
gO2/m2/d
cal/(cm2 d)
cal/(cm2 d)
gN/m2/d
gO2/m2/d
gP/m2/d
gO2/m2/d
gD m2 d1
cal/(cm2 d)
cal/(cm2 d)
/d

/d
/d
/d
/d
/d
/d
/d
/d
/m1
/m
/d
mole/(L atm)
/d
/d
mgN/m3
mgN/m3
July 16, 2004

khp(T)
KL12
KLb
KLp
KM,Dp
kna(T)
KNH4
KNH4,O2
kPOC,G1
krb(T)
krp(T)
ksNb
ksNp
Ksocf
Ksodn
Ksona
ksPb
ksPp
Kw
Lat
Llm
localTime
Lsm
m
mgY
mi
mi
mo
mo
n
na
na
nau
nfac
NH4,i
nn
nn

ammonium
temperature-dependent organic phosphorus
hydrolysis rate
pore water diffusion mass transfer coefficient
bottom algae light parameter
phytoplankton light parameter
oxygen half-saturation constant for bioturbation
temperature-dependent nitrification rate for
ammonia nitrogen
ammonium half-saturation constant
oxygen half-saturation constant
the mineralization rate of labile POC
temperature-dependent bottom algae respiration rate
temperature-dependent phytoplankton respiration
rate
nitrogen half-saturation constant for bottom algae
nitrogen half-saturation constant for phytoplankton
parameter for oxygen dependency of fast CBOD
oxidation
parameter for oxygen dependency of denitrification
parameter for oxygen dependency of nitrification
phosphorus half-saturation constant for bottom algae
phosphorus half-saturation constant for
phytoplankton
acidity constant for dissociation of water
latitude
longitude of local meridian
local standard time
longitude of standard meridian
optical air mass
mass of element Y
inorganic suspended solids
the solids concentration in sediment layer i
detritus
detritus concentration
Manning roughness coefficient
ammonia nitrogen
the ammonium concentration in the overlying water
unionized ammonia nitrogen
atmospheric turbidity factor
the concentration of total ammonium in sediment
layer i
nitrate nitrogen
nitrate concentration in the overlying water

/d
m/d
ly/d
gO2/m3
/d
gN/m3
mgO2/L
d1
/d
/d
gN/L
gN/L

gP/L
gP/L
radians
degrees
minutes
degrees
dimensionless
mg
mgD/L
gD/m3
mgD/L
gD/m3
mgN/L
mgN/m3
mgN/L
dimensionless
gN/m3
mgN/L
mgN/m3

108

no
NO3,i
npai
npsi
NSOD
o
o
oi1
ocrit
os(T, elev)
P
Pab
pai
Pap
PAR(z)
patm
pCO2
pi
pi
po
PO4,i
POC2,G1
POCR
psi
pwc
Q
Qab,i
Qi
Qin,i
Qnpa,i,j
Qnps,i,j
Qpa,i,j
Qps,i,j
QUAL2K

organic nitrogen
nitrate concentration in layer i
total number of non-point abstractions outflows
from reach i
total number of non-point sources inflows to reach i
the amount of oxygen demand generated by
nitrification
dissolved oxygen
the dissolved oxygen concentration in the overlying
water
oxygen concentration entering a reach below a dam
critical oxygen concentration for sediment
phosphorus sorption
saturation concentration of oxygen at temperature,
T, and elevation above sea level, elev
wetted perimeter
preference for ammonium as a nitrogen source for
bottom algae
total number of point abstractions from reach i
preference for ammonium as a nitrogen source for
phytoplankton
photosynthetically available radiation (PAR) at
depth z below water surface
atmospheric pressure
atmospheric partial pressure of carbon dioxide
inorganic phosphorus
the inorganic phosphorus in the overlying water
organic phosphorus
the concentration of total inorganic phosphorus in
sediment layer i
the concentration of the labile fraction of POC in the
anaerobic sediment layer
reference G1 concentration for bioturbation
total number of point sources to reach i
mean daily atmospheric precipitable water content
flow
total outflow from reach due to point and nonpoint
abstractions
outflow from reach i into reach i + 1
total inflow into reach from point and nonpoint
sources
jth non-point abstraction outflow from reach i
jth non-point source inflow to reach i
jth point abstraction outflow from reach i
jth point source inflow to reach i
109

mgN/L
gN/m3
dimensionless
dimensionless
gO2/m2/d
mgO2/L
gO2/m3
mgO2/L
gO2/m3
mgO2/L
m
dimensionless
dimensionless
dimensionless
ly/d
mm Hg
atm
gP/L
mgP/m3
gP/L
gP/m3
gO2/m3
gC/m3
dimensionless
m3/s or m3/d
m3/d
m3/d
m3/d
m3/d
m3/d
m3/d
m3/d
July 16, 2004

r
rcndn
rd
rda
RL
roc
roca
rocn
ron
ron'
ron
Rs
S
s
s
S0
Sb,i
Si
SOD
SODs
SODt
ss
t
T
T
T,w,f
Ta
Tair
Tair,f
Td

normalized radius of earths orbit (i.e., ratio of

actual earth-sun distance to mean earth-sun distance
ratio of oxygen equivalents lost per nitrate nitrogen
that is denitrified
ratio of deficit above and below dam
the ratio of dry weight to chlorophyll a
longwave reflection coefficient
ratio of oxygen consumed per organic carbon
oxidized to carbon dioxide
ratio of oxygen generated per organic carbon
produced by photosynthesis when nitrate is taken up
ratio of oxygen generated per organic carbon
produced by photosynthesis when ammonia is taken
up
the ratio of oxygen to nitrogen consumed during
nitrification
ratio of oxygen consumed per ammonia nitrogen
converted by nitrification/denitrification to nitrogen
gas
the ratio of oxygen to nitrogen consumed for total
conversion of ammonium to nitrogen gas via
nitrification/denitrification
albedo or reflectivity (fraction of solar radiation that
is reflected)
channel slope
chloride
mass transfer coefficient between the water and
the aerobic sediments
bottom slope
sources and sinks of constituent due to reactions for
bottom algae
sources and sinks of constituent due to reactions and
mass transfer mechanisms for water constituents
the sediment oxygen demand
the supplemental sediment oxygen demand
total sediment oxygen demand = SOD + SODs
channel side slope
time
water temperature
water temperature
water temperature
absolute temperature
air temperature
air temperature
dew-point temperature

dimensionless
gO2/gN
dimensionless
gD/mgA
dimensionless
gO2/gC
gO2/gC
gO2/gC
= 4.57 gO2/gN
gO2/gN
= 1.714 gO2/gN
dimensionless
dimensionless
mgCl/L
m/d
m/m
gD/m2/d
g/m3/d or
mg/m3/d
gO2/m2/d
gO2/m2/d
gO2/m2/d
m/m
d
o
C
o
C
o
F
K
o
C
o
F
o
C

110

Ti
timezone
Tnps,i,j
Tps,i,j
trueSolarTim
e
Ts,i
tsr
tss
Tstd
tt,i
U
Ui*
Uw
Uw,mph
Uw,z
va
va
vdt
vdt
vi
Vi
vp
vpc
W0
w2
Wh,i
Wi
x
zw

QUAL2K

temperature in reach i
time zone indicates local time zone in relation to
Greenwich Mean Time (GMT) (negative in western
hemisphere)
jth non-point source temperature for reach i
jth point source temperature for reach i
time determined from actual position of the sun in
the sky
temperature of bottom sediment
time of sunrise
time of sunset
standard time
travel time from headwater to end of reach i
mean velocity
shear velocity
wind speed
wind speed
wind speed at height zw above water surface
phytoplankton settling velocity
phytoplankton settling velocity
detritus settling velocity
detritus settling velocity
inorganic suspended solids settling velocity
volume of ith reach
pathogen settling velocity
non-living particulate organic carbon settling
velocity
solar constant
the burial velocity
net heat load from point and non-point sources into
reach i
external loading of constituent to reach i
pathogen
height above water for wind speed measurements

111

C
hours
o

C
C
minutes
o

C
Hr
Hr
Hr
D
m/s
m/s
m/s
mph
m/s
m/d
m/d
m/d
m/d
m/d
m3
m/d
m/d
2851 cal/cm2/d
m/d
cal/d
g/d or mg/d
cfu/100 mL
m

July 16, 2004

Greek:
Symbol

d
s
0
1
2
i

o
p
pn

PO4,1
v

ts
xi

clear

sky
a
Lb
Lp
Nb
Np
p

Definition
depth rating curve coefficient
suns altitude
suns altitude
sediment thermal diffusivity
fraction of total inorganic carbon in carbon dioxide
fraction of total inorganic carbon in bicarbonate
fraction of total inorganic carbon in carbonate
effect of inorganic suspended solids on light
attenuation
effect of particulate organic matter on light
attenuation
linear effect of chlorophyll on light attenuation
non-linear effect of chlorophyll on light attenuation
depth rating curve exponent
solar declination
factor that increases the aerobic sediment layer
partition coefficient relative to the anaerobic
coefficient
virtual temperature difference between the water
and air
difference between standard and local civic time
length of ith reach
emissivity of water
emissivity of longwave radiation from the sky with
no clouds
emissivity of longwave radiation from the sky with
clouds
estimated error
bottom algae light attenuation
phytoplankton light attenuation
bottom algae nutrient attenuation factor
phytoplankton nutrient attenuation factor
phytoplankton photosynthesis rate
density of water
Stefan-Boltzmann constant
local hour angle of sun
residence time of ith reach
temperature coefficient for zero and first-order
reactions

Units
dimensionless
radians
degrees
cm2/s
dimensionless
dimensionless
dimensionless
L/mgD/m
L/mgD/m
L/gA/m
(L/gA)2/3/m
dimensionless
radians
dimensionless
F
hr
m
dimensionless
0-1
0-1
%
0-1
0-1
0-1
0-1
/d
g/cm3
11.7x10-8 cal/(cm2 d K4)
radians
d
dimensionless

112

am
12
ai
pi
CH4
Dd
Dp
NH4
NO3
POC,G1
CH4,1
NH4,1
NO3,i

QUAL2K

elevation adjusted optical air mass

the bioturbation mass transfer coefficient between
the sediment layers
the partition coefficient for ammonium in sediment
layer i
the partition coefficient for inorganic phosphorus in
sediment layer i
temperature correction factor for sediment methane
oxidation
temperature coefficient for porewater diffusion
temperature coefficient for bioturbation diffusion
temperature correction factor for sediment
nitrification
sediment denitrification temperature correction
factor
temperature correction factor for labile POC
mineralization
the reaction velocity for methane oxidation in the
aerobic sediments
the reaction velocity for nitrification in the aerobic
sediments
denitrification reaction velocity sediment layer i

113

m/d
m3/gD
m3/gD
dimensionless
dimensionless
dimensionless
dimensionless
dimensionless
dimensionless
m/d
m/d
m/d

July 16, 2004

APPENDIX C: SEDIMENT-WATER HEAT

EXCHANGE
Although the omission of sediment-water heat exchange is usually justified for deeper systems, it can
have a significant impact on the heat balance for shallower streams. Consequently, sediment-water heat
exchange is included in QUAL2K.
A major impediment to its inclusion is that incorporating sediment heat transfer often carries a heavy
computational burden. This is because the sediments are usually represented as a vertically segmented
distributed system. Thus, inclusion of the mechanism results in the addition of numerous sediment
segments for each overlying water reach.
In the present appendix, I derive a computationally-efficient lumped approach that yields comparable
results to the distributed methods.

The conduction equation is typically used to simulate the vertical temperature distribution in
a distributed sediment (Figure 24a)
T
2T
2
t
x

(310)

This model can be subjected to the following boundary conditions:

T (0, t ) T Ta cos (t )
T ( , t ) T

where T = sediment temperature [oC], t = time [s], = sediment thermal diffusivity [m2 s1], and
z = depth into the sediments [m], where z = 0 at the sediment-water interface and z increases
downward, T = mean temperature of overlying water [oC], Ta = amplitude of temperature of
overlying water [oC], = frequency [s1] = 2/Tp, Tp = period [s], and = phase lag [s]. The first
boundary condition specifies a sinusoidal Dirichlet boundary condition at the sediment-water
interface. The second specifies a constant temperature at infinite depth. Note that the mean of the
surface sinusoid and the lower fixed temperature are identical.

Page 114

z
(a) distributed

(b) Lumped

Figure 24. Alternate representations of sediments: (a) distributed and (b) lumped.

Applying these boundary conditions, Eq. (231) can be solved for (Carslaw and Jaeger 1959)
T ( z , t ) T Ta e ' z cos (t ) ' z

(311)

where [m1] is defined as

'

(312)

The heat flux at the sediment water interface can then be determined by substituting the
derivative of Eq. (232) into Fouriers law and evaluating the result at the sediment-water
interface (z = 0) to yield
J (0, t ) C p Ta cos (t ) / 4

(313)

where J(0, t) = flux [W/m2].

An alternative approach can be developed using a first-order lumped model (Figure 24b),
H s s C ps

dTs s s C ps
T Ta cos (t ) Ts

dt
Hs / 2

where Hsed = the thickness of the sediment layer [m], s = sediment density [kg/m3], and Cps =
sediment heat capacity [joule (kg oC)]1]. Collecting terms gives,

Page 115

dT
k h T k h T k hTa cos (t )
dt

where

kh

2 s
H sed

After initial transient have died out, this solution to this equation is

T T

kh
kh 2
2

Ta cos (t ) tan 1 ( / k h )

(314)

which can be used to determine the flux as

2
J
C p Ta cos (t )

H sed

kh
2

kh

cos (t ) tan ( / k h )
1

(315)

It can be shown that Eqs. (232) and (235) yield identical results if the depth of the single layer
is set at
H sed

1
'

(316)

Water quality models typically consider annual, weekly and diel variations. Using = 0.0035
cm2/s (Hutchinson 1957), the single-layer depth that would capture these frequencies can be
calculated as 2.2 m, 30 cm and 12 cm, respectively.
Because QUAL2K resolves diel variations, a value on the order of 12 cm should be selected
for the sediment thickness. We have chosen of value of 10 cm as being an adequate first estimate
because of the uncertainties of the river sediment thermal properties (Table 4).

Page 116