United States Office of Water (4305) EPA-823-B-05-001

Environmental Protection October 2005

Agency

AQUATOX (RELEASE 2.1)

MODELING ENVIRONMENTAL FATE

AND ECOLOGICAL EFFECTS IN

AQUATIC ECOSYSTEMS

VOLUME 3: USER’S MANUAL FOR THE

BASINS (VERSION 3.1) EXTENSION TO

AQUATOX RELEASE 2.1

AQUATOX (RELEASE 2.1)

MODELING ENVIRONMENTAL FATE

AND ECOLOGICAL EFFECTS

IN AQUATIC ECOSYSTEMS

VOLUME 3: User's Manual for the BASINS (Version 3.1)

Extension to AQUATOX Release 2.1

Jonathan S. Clough

OCTOBER 2005

U.S. ENVIRONMENTAL PROTECTION AGENCY

OFFICE OF WATER

OFFICE OF SCIENCE AND TECHNOLOGY (MAIL CODE 4305T)

WASHINGTON DC 20460
ii

DISCLAIMER

 This document has been approved for publication by the Office of Science and Technology, Office

of Water, U.S. Environmental Protection Agency. Mention of trade names, commercial products

or organizations does not imply endorsement or recommendation for use.

This document describes an enhanced version of an ecosystem simulation model. It is not intended

to serve as guidance or regulation, nor is the use of this model in any way required. This document

cannot impose legally binding requirements on EPA, States, Tribes, or the regulated community.

ACKNOWLEDGMENTS

The BASINS Extension to the AQUATOX model has been developed by Dr. Richard A. Park of

Eco Modeling; the AQUATOX-side programming, documentation, and additional linkage

development was performed by Jonathan S. Clough of Warren Pinnacle Consulting, Inc. under

subcontract to Eco Modeling. Additional linkage development and the programming of the

WinHSPF and ArcView interfaces within BASINS was performed by Paul Duda of AQUA TERRA

Consultants. The BASINS Extension was funded with Federal funds from the U.S. Environmental

Protection Agency, Office of Science and Technology under contract number 68-C-01-0037 to

AQUA TERRA Consultants, Anthony Donigian, Work Assignment Manager.

The assistance, advice, and comments of the EPA work assignment manager, Marjorie Coombs

Wellman of the Exposure Assessment Branch, Office of Science and Technology have been of great

value in developing this extension and preparing this report. 
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TABLE OF CONTENTS

DISCLAIMER . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ii

ACKNOWLEDGMENTS ...................................................... ii

1 INTRODUCTION TO THE BASINS AQUATOX EXTENSION ................ 1-1

1.1 Overview and Background ........................................ 1-1

1.2 System Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-3

2 WINHSPF TO AQUATOX LINKAGE ......................................... 2-1

2.1 Introduction .................................................... 2-1

2.2 Selection of Pollutants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-5

2.3 AQUATOX Linkage ............................................. 2-6

2.4 Obtain HSPF Watershed Simulation ................................. 2-7

2.5 Running AQUATOX from WinHSPF ................................ 2-7

2.6 Linked Simulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-12

2.7 Specification of Additional State Variables and Loadings . . . . . . . . . . . . . . . 2-13

2.8 Run AQUATOX and Plot Results .................................. 2-21

3 BASINS GIS TO AQUATOX LINKAGE ....................................... 3-1

3.1 Introduction .................................................... 3-1

3.2 Performing the BASINS to AQUATOX Linkage ....................... 3-1

3.3 Using AQUATOX after a BASINS to AQUATOX Linkage .............. 3-5

4 SWAT TO AQUATOX LINKAGE ............................................ 4-1

4.1 Introduction: .................................................... 4-1

4.2 Running a SWAT Simulation ...................................... 4-1

4.3 Loading SWAT data into AQUATOX ............................... 4-4

4.4 The Linkage Process . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-7

5 AQUATOX TO GENSCN LINKAGE .......................................... 5-1

5.1 Introduction .................................................... 5-1

5.2 Linking to GenScn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-1

5.3 Using GenScn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-1

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1 INTRODUCTION TO THE BASINS AQUATOX EXTENSION

1.1 Overview and Background 

It has become increasingly apparent that methods and tools are needed to analyze the combined fate

and effects of all stressors on aquatic ecosystems from all sources. Stressors may include nutrients,

organic loading, toxic organic compounds, sediments and habitat alteration; sources include point

and non point source loadings and atmospheric deposition. Stressors may affect water clarity, algae

populations, dissolved oxygen levels, fish and invertebrate communities, levels of contaminants

in fish tissue, and many other important environmental conditions. Management approaches that

focus on one stressor at a time may miss important interactions that could determine whether overall

environmental goals, such as restoration of a more natural aquatic ecosystem, are met. 

Environmental management programs and activities that could benefit from additional tools for an

integrated approach include water quality criteria and standards, Total Maximum Daily Loads

(TMDLs), identification of the cause(s) of biological impairment where there are multiple stressors,

and ecological risk assessments.

AQUATOX is a time-variable ecological risk assessment model that simulates the fate and effects

of various environmental stressors in aquatic ecosystems. It simulates the fate and transfer of

pollutants from loads to the water, sediments, and biotic components, and transfer throughout the

food web. Simultaneously it predicts the effects of the stressors on the ecosystem, by simulating the

chemical, physical and biological processes that bind the ecosystem together. AQUATOX can

predict the fate and ecological effects of nutrients, organic toxicants, and bioaccumulative

compounds, as well as the expected ecosystem responses to pollution reductions. It considers

several trophic levels, including attached and planktonic algae and submerged aquatic vegetation,

invertebrates, and forage, bottom-feeding, and game fish; it also represents associated organic

toxicants.

BASINS (Better Assessment Integrating Point and Nonpoint Sources) is a combined GIS/water

quality modeling system that includes numerous national level environmental and cartographic data

layers, analytical tools, watershed loading models, and instream water quality models. One of the

main advantages of an integrated system such as BASINS is that the time consuming task of

developing input data files for the various models is reduced: watershed characteristics necessary

for the watershed models can be developed from the landscape data layers, and data can be

converted into the proper formats for model input files. BASINS Version 3 changed the system

architecture to a modularized system, and converted the models and many other functions to

ArcView "extensions." The modular setup allows the models to run either as part of BASINS or

stand alone. The modularity also makes it easier to add components, and for users to customize

BASINS for their own purposes. This new software extension links the AQUATOX ecosystem

model to the BASINS modeling system.
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The extension has been developed to assist in comprehensive environmental analysis and prediction.

 When linked to BASINS, AQUATOX can be used to track ecological effects of point and non

point source loadings of organic and nutrient loadings, organic chemicals and pesticides, and

changes in hydrology. Specifically, the extension has been designed so that AQUATOX can be run

with site characteristics and loadings input directly from the BASINS GIS data layers or from the

HSPF and SWAT watershed models. The extension makes possible the direct linkage of the

following types of data from BASINS to AQUATOX:

• Site Physical Characteristics (source: GIS Layer, HSPF, SWAT)

• Dynamic Water Volume Data (source: HSPF, SWAT)

• Nutrient & BOD time-series Loadings (source: HSPF, SWAT)

• Organic Chemical or Pesticide Loadings (source: HSPF, SWAT)

• Time Varying TSS Concentrations (source: HSPF, SWAT)

For each of the time-series that are linked, the extension converts units and integrates data to an

appropriate time-step automatically. Additionally, the extension allows AQUATOX output to be

linked to GenScn, the post-processor within BASINS. GenScn offers several statistical functions

that are not available through the AQUATOX output screen such as comparison of predicted and

observed time-series and duration analysis.
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Linkages Between Models

BASINS GIS Layer

HSPF

Previously Existing Linkage New Linkage

SWAT

AQUATOX

GenScn

The following diagram illustrates how the BASINS AQUATOX extension integrates AQUATOX

into the previously existing BASINS framework:

1.2 System Requirements

The BASINS AQUATOX extension requires Microsoft Windows 98, NT, 2000, or XP. Because

ArcView and the constituent models are resident in memory, 256 MB of RAM or higher is highly

recommended. A user may be able to use the extension with less RAM by setting up a significant

virtual memory file within the Windows control panel, although that will necessitate frequent disk

access and increase simulation run times. See section 3 of the BASINS 3.0 Users Manual (EPA-823-

B-01-001, or see the BASINS web site at http://www.epa.gov/OST/BASINS/ ) for more information

about BASINS Hardware and software requirements. Within BASINS, ArcView's Spatial Analyst

extension is required to run the SWAT model and to automatically delineate rivers within the

BASINS modeling system.
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2 WINHSPF TO AQUATOX LINKAGE

2.1 Introduction

Data from HSPF (Hydrological Simulation Program- FORTRAN) can be linked to the AQUATOX

ecosystem model through the BASINS AQUATOX Extension. HSPF is a model that simulates the

hydrologic processes, and associated water quality processes, on pervious and impervious land

surfaces and in streams and well-mixed impoundments. AQUATOX accepts data from HSPF

assuming that a single HSPF river reach is equivalent to a single AQUATOX riverine segment.

Using the results of an HSPF simulation, AQUATOX accepts input for the water volume of the

system, nutrient time-series loadings, organic chemical time-series loadings, and physical

characteristics of the system.

To link HSPF data to AQUATOX the following steps are undertaken:

• WinHSPF is executed

• An HSPF simulation is loaded from disk (or using the BASINS interface)

• Appropriate pollutants for linkage to AQUATOX are selected within WinHSPF

• The WinHSPF software is told to produce specialized AQUATOX output files

• The HSPF simulation is executed

• AQUATOX is invoked from the WinHSPF interface, causing the linkage process to

take place

• Additional parameters are specified within AQUATOX to complete the AQUATOX

simulation

• The AQUATOX simulation is run

To link HSPF data to AQUATOX, the WinHSPF interface must be used. WinHSPF provides an

interactive Windows interface for the HSPF model. WinHSPF assists the user in building UCI files

from GIS data, especially data from the BASINS system. This program can be found under the

BASINS Start menu as shown below.
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As an illustrative example, this documentation will walk through the steps required to link the

tutorial.uci file that comes with the BASINS installation set to AQUATOX. To ensure that this file

has not changed during previous uses of WinHSPF, we will start by using the “Create” option to

restore the tutorial.uci file to its original state. (Note: If you wish to retain your existing tutorial.uci

file, please backup the file found in the /basins/data/tutorial/hspf directory to a different name.)

To open the create project window within WinHSPF go to the “File” menu and select “Create.” The

Create Project window contains Select buttons for three types of files, a list for selecting a

meteorological station (met station), and a set of radio buttons for choosing between two land

surface segmentation options. 
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Start by selecting the tutorial watershed file. Select the “BASINS\data\tutorial\HSPF\tutorial.wsd”

file as shown above. Next, select the Met WDM file. Select the “BASINS\data\met_data\

tutorial.wdm” file. Finally, specify the project WDM file. This file is used to store model output

and does not have to be a previously existing file.

Once the met WDM file has been specified, the “Initial Met Station” list will be populated with the

identifier corresponding to met stations available for use in the new HSPF project. One item from

this list should be selected in order to have some met data included in the HSPF simulation. Select

the first met station on the list (Johnstown) as shown above.

In the Model Surface Segmentation radio buttons, the Grouped option creates a single model

segment for all collective subbasins, and the Individual creates a single model segment for each

subbasin. For this tutorial leave the selection set to Grouped. Then click the OK button to call the

algorithms that build the new UCI file. The new UCI file will be written to the

“BASINS\data\tutorial\HSPF\” directory. 

For more information on using the “Create” screen within WinHSPF, see Lesson 1 in the Tutorial

within the WinHSPF manual (found in the BASINS\docs directory).
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After you have left the “Create” screen, the UCI file will have been created and opened. In the

future, you may open this UCI by clicking on “File,” then “Open.,” and then selecting the file.
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2.2 Selection of Pollutants

In order to pass water quality data to AQUATOX, a user must include several water quality

categories within their HSPF simulation. Click on the Pollutant Selection button. Add NH3, NO2

and NO3, Ortho P, BOD, DO, and Sediment. Click “OK” when finished.
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2.3 AQUATOX Linkage

Specify AQUATOX output by clicking on the Output Manager button, choosing the “AQUATOX

Linkage” radio button, and clicking on “Add.” Choose one or more reaches in the next dialog, click

“OK,” and “Close.” (Note: If “AQUATOX linkage”is not visible in the Output Manager window,

then the AQUATOX extension has not been installed. Obtain a copy of the AQUATOX extension

and install it. To do this, the file “b3mo_aquatox.avx” must be obtained and installed into the

BASINS\etc\Extensions\Models\ directory) 
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The above dialog box appears when you have chosen to add an AQUATOX output location. If

using WinHSPF “build 2.3 revision 1” or higher, when adding AQUATOX output, there will be

options to output time-series on an hourly or a daily basis. AQUATOX release 2.1 allows only

daily time-series to be imported so this feature is not relevant to Release 2.1. If hourly data are

chosen, AQUATOX Release 2.1 will aggregate the hourly data into daily values. Future

versions of AQUATOX will allow the input of hourly time-steps so this feature is provided for

forward compatibility.
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2.4 Obtain HSPF Watershed Simulation

Click on the Run HSPF button to obtain a simulation of the watershed. 

2.5 Running AQUATOX from WinHSPF

From the Functions menu choose AQUATOX.
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In the WinHSPF-AQUATOX Linkage dialog window, select the reach to link (only one at a

time). Also, check to make sure the BASINS Watershed File is specified. If you are running the

tutorial and WinHSPF does not find the default, use “tutorial.wsd” from

\basins\data\tutorial\hspf\. Otherwise, choose the Watershed File that is relevant to the HSPF

simulation you are running. If no watershed file is specified, AQUATOX will not be able to

locate the BASINS GIS files that are relevant to this particular HSPF simulation. In this case,

Channel Length, Channel Slope, Channel Depth, and Maximum Depth data will not be read from

the GIS data.

To initiate AQUATOX, click the “Start AQUATOX” button. (If AQUATOX was installed after

BASINS, you may need to locate the “AQUATOX.EXE” program file in the “PROGRAM”

directory of your AQUATOX installation.) After AQUATOX has started, you will be asked if

you wish to create a new simulation or modify an existing AQUATOX simulation. To continue

stepping through this tutorial, you should choose a “blank” simulation.
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If you choose to use a “blank” simulation, the only parameters within the AQUATOX simulation

will be taken from the BASINS linkage. If you choose to modify an existing AQUATOX

simulation, data from BASINS will be used to overwrite variables and time-series from the

original simulation. Note: if you choose to modify an existing AQUATOX simulation,

AQUATOX will rename the file-name of the simulation so that the original simulation remains

intact. You will be able to see exactly which variables in the original simulation were

overwritten by examining the linkage log file as discussed below. 

Choosing “modify existing simulation” is often useful because the HSPF-AQUATOX linkage

does not pass any information about plants or animals in the system. Therefore a user can take

an existing AQUATOX simulation with extensive information about plants and animals and see

how it will respond to the flow, nutrient, and toxicant regime found in the BASINS simulation.

Additionally, a user can perform experiments and see how a particular set of plants and animals

will respond to a different set of flow and nutrient parameters from different reaches within

BASINS or different calibrations of the same BASINS river reach.

Next, you will be asked for which dates you wish to import loadings from the HSPF simulation.
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If the HSPF simulation is fairly long in duration, you may wish to reduce the amount of loadings

you bring into AQUATOX. The more years of loadings that you import into AQUATOX, the

longer the linkage process will take, the larger the AQUATOX simulation will be on disk, and

the slower the AQUATOX simulation will run. 
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If using WinHSPF “build 2.3 revision 1” or higher, you will next see the above dialog box

asking for the characterization of phosphate as modeled in HSPF. Total Phosphate in HSPF

includes dissolved orthophosphate, adsorbed orthophosphate, and organic phosphate. These

compartments need to be transformed into bioavailable phosphate within AQUATOX. To do

this, you can choose which of the HSPF forms of phosphate to link, choose a bioavailable

fraction, and also select whether the phosphate being linked best represents Total Soluble P or

Total P. If you don’t have any particular information about the bioavailability of the phosphate

you are modeling in HSPF, a reasonable assumption is to pass all phosphate forms and use the

Total P linkage as shown above. Choosing a bioavailable fraction of 1.0, as shown above,

indicates that all phosphate being passed is bioavailable (perhaps through P-solubilizing bacterial

action).

When using earlier versions of WinHSPF, dissolved orthophosphate is the only form of

phosphate that is automatically passed into AQUATOX.
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Next you will need to characterize the organic matter loadings that are being read into

AQUATOX from HSPF. AQUATOX models organic matter in the water column as four

compartments by splitting organic matter into refractory and labile fractions and dissolved and

particulate fractions. 

AQUATOX has a single parameter that characterizes the percentage of inflow loadings that are

labile versus refractory. This parameter remains constant throughout the course of an

AQUATOX simulation. From HSPF, AQUATOX can obtain two different daily loadings (BOD

and refractory organic carbon) with different refractory to labile splits. BOD is assumed to be

mostly labile in nature, while refractory organic carbon is refractory by definition. If a user has

additional information about the refractory and labile split of BOD modeled within HSPF, the

next dialog screen allows this information to be incorporated into the linkage. To get the best

representation of organic matter coming into the system, the linkage software sums these two

loadings. Then, using a weighted average, AQUATOX determines the most representative

percentage of labile vs. refractory for this total mass of incoming organic matter. In this manner,

the total labile and refractory loadings will be averaged out over the course of the entire

AQUATOX simulation.

Organic matter loadings must also be broken down into particulate and dissolved fractions for

use in AQUATOX. This percentage may also be entered in the dialog screen shown below. The

default value of 10% particulate is a generally accepted percentage, but this can vary depending

on site-specific conditions.
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2.6 Linked Simulation

At this point, the linkage procedure should complete itself and the below screen will be

displayed. You may wish to click on “View Log File” to see what actions were taken; the log

file name and location is also copied into the set of notes associated with the AQUATOX study. 

These notes can be displayed by clicking on the “Notes” button from that main study screen

(Note: the Notes button is not available when the linkage windows or the Wizard is open).
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2.7 Specification of Additional State Variables and Loadings

Especially if linking to a blank simulation, the user is advised to click the “Continue to Wizard”

button to facilitate specification of state variables and loadings that are not available from the

linkage. There are 19 steps with context-sensitive help. Unless discussed below, the default

values are appropriate for the initial simulation. This section will discuss how a user can set up

the basic ecosystem variables after linking to a blank simulation. You may also reference the

AQUATOX Users Manual (EPA-823-R-04-001) for more information on using the AQUATOX

wizard.
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Note: While the AQUATOX linkage reads BOD data from HSPF, it converts these data into

organic matter and then adds the data to the time-series of refractory organic carbon data for a

complete set of organic carbon loadings. Therefore, the user should maintain a selection of

“organic matter” in Wizard Step 4.

For a typical stream you should add Diatoms, periphytic Diatoms, Greens, and Blue-greens, and

Macrophytes. Set their initial conditions to 1 g\m2 in a subsequent screen (unless of course you

have site specific data). You should run the model for several years to “spin up” the model and

avoid transient conditions from the initial guesses; you can then take the end conditions and

substitute them for the original initial conditions in subsequent simulations.
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Several invertebrates should be chosen, and their initial conditions also set to 1, as shown.

Likewise, several fish would usually be chosen. Initial conditions of 0.2 g\m2 are suggested.
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In the wizard step 8, site characteristics that have been imported from HSPF will be displayed. 

Note that the stream bottom is assumed to be 100% run. If the site has significant riffle and pool

features, change these parameters accordingly.

Next, water volume data will be loaded from HSPF so that the water volume in the AQUATOX

reach is identical to the HSPF water volume over the course of the simulation. To make this

possible, the inflow water loaded into AQUATOX has been adjusted for the evaporation and

precipitation predicted by HSPF. 

To use the HSPF water volume data, the “Vary Given Inflow and Outflow” option should remain

checked as shown below. For more information about the other water volume modeling choices

on this screen, you can select the “Help” button from this wizard step.
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Because a time-series of water temperature is generally imported from the HSPF linkage, the

user should select the option "Use time-varying temperature" in Wizard Step 10.

Stream simulations are generally not sensitive to wind, so use the default with a mean value of 3

m\s.

Wizard step 14 displays inorganic solids loadings within the AQUATOX simulation. Currently

TSS concentrations are linked from HSPF as the summation of modeled sand, silt, and clay. 

TSS concentrations can affect light extinction within a simulation, affecting algal growth. A

user can also choose to model sand, silt, and clay as state variables within AQUATOX, but not

directly through the linkage at this time. (As light extinction is currently the only feedback

between inorganic sediments and modeled biota, HSPF simulated TSS concentrations provide a

sufficient source of data. In the future, if more complex feedbacks between sand silt and clay

and the biotic components within AQUATOX are developed, linkage to categorized sand, silt,

and clay data from HSPF will be appropriate.)
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Oxygen loadings have been converted from kg\hr as predicted by HSPF into mg\L of inflow

water for integration into the AQUATOX interface. Because of this translation, the oxygen

concentration predicted within the AQUATOX reach will be essentially identical to the oxygen

concentration predicted by HSPF. Because of the translation from kg\hr to mg\L of inflow

water, in some cases the inflow loading value may appear to be too high within AQUATOX. 

However, when these loadings are brought into the system, and matched with the volume of

inflow water in that time-step, the oxygen concentration within the AQUATOX reach will match

the oxygen concentration predicted by HSPF at that time.

Inflow loadings serve two purposes: they can be realistic time-series predicted by HSPF, or they

can be “seed” values to account for colonization and recruitment. The recommendation is to use

loadings of 0.00001 for plants, fish, and invertebrates other than insects. A value of 0.0001 is

suggested for insects to account for drift and eggs from free-flying adults.
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There are usually many modeled components of the water that directly flow into each

AQUATOX simulation. This wizard step is provided so that you may check and edit inflow

loadings for each of these inflow components. You can scroll through the list to see which of

these items have already had dynamic data loaded into them from the HSPF to AQUATOX

linkage. As mentioned above, for several of the new animals you added to the simulation within

the wizard, a “seed” loading may also be appropriate.
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2.8 Run AQUATOX and Plot Results

Run the model for several years and plot the results to see what changes may need to be made.

The “Change Variables” button allows you to select which AQUATOX variables are currently

plotted and whether to plot variables on one or two axes. For further information on the

AQUATOX output capabilities, please see the Users’ Manual (referenced below).

(Note: Plotted results above are given as an example only. Your results will vary depending on the

specific data libraries utilized, the stream reach modeled and the initial conditions chosen)

A site-specific parameter that often needs to be adjusted is mortality for the fish. As mentioned

previously, it may be desirable to take the end biomass values and use them as initial conditions

to avoid a transient response in the first year or two due to inappropriate values. In this

example, all fish started with initial conditions that are too high, and the shiners and stonerollers 

attained even higher levels before crashing. (Reasons for the decline can be determined by

saving and plotting the rates.) The decline of all state variables toward the end of the simulation

is the result of declining water levels. 
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For more information on how to use AQUATOX see:

AQUATOX (Release 2)--Modeling Environmental Fate and Ecological Effects in Aquatic

Ecosystems. Volume 1: User's Manual, January 2004, 823-R-04-001.

It is available on-line at: http:\\www.epa.gov\waterscience\models\aquatox\
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3 BASINS GIS TO AQUATOX LINKAGE

3.1 Introduction

A user may link data from the BASINS GIS data layer directly to AQUATOX through the

ArcView interface. This can be helpful for gathering information about a site even when there is

no related HSPF or SWAT simulation. The categories of data that are relevant to AQUATOX

within the BASINS GIS layers are listed below:

• Reach Name

• Channel Length

• Mean Depth of Reach

• Channel Slope

• Channel Depth

The steps that are required to link BASINS GIS data to AQUATOX are as follows

• Verify that the AQUATOX and delineation extensions are active.

• Manually or automatically delineate the watershed sub-basins.

• Select the stream segment to be modeled within AQUATOX.

• Execute AQUATOX from the BASINS interface.

• Setup and Run the AQUATOX simulation.

3.2 Performing the BASINS to AQUATOX Linkage

Performing this linkage is very similar to linking a stream reach from the BASINS GIS data

layer to HSPF, except that it starts from the BASINS interface rather than the WinHSFP

interface. The following steps are required:
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Open a BASINS project by selecting BASINS from the “Programs” menu as shown.

Open “TUTORIAL.APR” or whichever BASINS project file you wish to work with.

Next, verify that the AQUATOX extension is active in your BASINS project by typing Ctrl+B

from the BASINS View and selecting the Models item from the Extension Categories drop-down

list. The AQUATOX entry in the BASINS Extensions list should be visible and selected.
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If AQUATOX is not visible in the BASINS Extensions list when the Models item has been

selected, then the AQUATOX extension has not been installed. Obtain a copy of the AQUATOX

extension and install it. (To do this, the file “b3mo_aquatox.avx” must be obtained and installed

into the BASINS\etc\Extensions\Models\ directory) 

If AQUATOX is not selected (checked), click on it to select it. 

Also, to use the AQUATOX extension to create an AQUATOX simulation, you must first run

the manual or automatic delineation extensions to create the watershed, sub-basins, streams, and

outlets themes. See section 8 of the BASINS User Manual for details on watershed delineation. 

This step requires that the automatic or manual watershed delineation tools are selected in the

“Delineate” extension category within the BASINS Extension Manager. (Note: automatic

delineation requires the ArcView Spatial Analyst software package.)

When delineating the watershed sub-basins, a user should keep in mind that the primary stream

in each sub-basin will become the AQUATOX reach simulated. On an ecological basis, fastflowing upstream river segments may be significantly different than downstream slow-flowing
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backwaters. Therefore, a user should try to keep the size of the reaches small enough so that

dramatically different ecosystems are not simulated within a single AQUATOX reach. 

After the watershed has been delineated, the user must select the stream segment that is to

become an AQUATOX stream simulation. Select the “streams” theme and use the “select

feature” tool to make the relevant stream reach turn yellow. Then, select AQUATOX from the

“Models” menu at the top of the screen.

As shown below, you will next be asked whether you wish to “Open AQUATOX with Linked

BASINS Stream data.” (Note: Screen capture based on TUTORIAL.APR)

Selecting “Yes from this dialog” will open AQUATOX with linked data. Selecting “No”will

open AQUATOX but with no linked data.

3.3 Using AQUATOX after a BASINS to AQUATOX Linkage
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As was the case for the HSPF linkage, a user may choose to link to a blank AQUATOX

simulation or overwrite relevant parameters and loadings in an existing AQUATOX simulation. 

See Section 2.5 for more information about this choice.

Next, the AQUATOX Linkage Information screen becomes visible. This screen shows the types

of information that have been linked to AQUATOX and the additional parameters that are

required to fully specify an AQUATOX simulation.

All parameters that are loaded from the GIS data layers are logged in a text file. The user may

view and print the log file from this screen by selecting the “View Log File” button. (If a user

wishes to refer to the log file at a later time, the location of this log file is written into the

“Notes” dialog, available through the main screen of the AQUATOX interface.) 
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An expert AQUATOX user may choose to bypass the user-friendly AQUATOX simulation setup

wizard. Beginning users are encouraged to continue to the wizard to finish specifying the

required parameters.
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4 SWAT TO AQUATOX LINKAGE

4.1 Introduction:

AQUATOX has the capability to read input and output data from SWAT (Soil and Water

Assessment Tool) version 2000. AQUATOX will read data about channel geometry, nutrient

and pesticide loadings, simulation period, water flow, and organic and inorganic sediment

loadings.

To perform this linkage, the following steps must take place.

• The user must complete the specification and calibration of a SWAT 2000 simulation

using the BASINS 3.0 interface. (This requires the ArcView Spatial Analyst software

package.)

• The user must start AQUATOX and select the SWAT output file that contains the

relevant data.

• The SWAT sub-basin the user wishes to gather data from will then be selected.

• AQUATOX will read all relevant data from the SWAT input and output files.

• Finally, the user is required to fill in AQUATOX parameters that are not available

through the SWAT linkage. 

When the process is complete an AQUATOX simulation that corresponds to the main channel

within a SWAT sub-basin will have been created. This SWAT to AQUATOX linkage process is

described in more detail below.

4.2 Running a SWAT Simulation

This section will outline some relevant points about running SWAT if a user intends to link the

SWAT simulation to the AQUATOX model. Complete documentation as to how to run the

SWAT 2000 model can be found in the B2SWAT.chm file located in the BASINS\DOCS

directory following the installation of BASINS 3.0. 

The steps required to run a SWAT model are roughly outlined below:

• Automatically delineate the watershed.

• Define land use and soil themes for the SWAT model

• Define the HRUs (hydrologic response units) distribution for the SWAT model

• “Edit Input” within the SWAT view

• Write all input data files within the SWAT view (under the “Input” menu)

• Run the SWAT model
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At each step of the above process, a user should bear in mind that the main reach within a single

SWAT sub-basin will later correspond to a single AQUATOX reach. This may affect a user’s

choices within the automatic delineation or input choices for the SWAT model. Smaller subbasins are generally most appropriate for an AQUATOX simulation so that the ecosystem does

not change dramatically within a single sub-basin.

When a user has completed all the steps required above, and has chosen to “Run SWAT,” the

following dialog box appears:

As can be seen from the lower left portion of this screen, the SWAT model can produce output in

“daily,” “monthly,” or” yearly” time steps. To link the model to AQUATOX, daily or monthly

time-steps must be chosen. Annual time-steps do not provide the data resolution required by

AQUATOX. 
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A user also can select the SWAT simulation period at the top of this screen. If the SWAT model

has many sub-basins and is being run for many years, choosing monthly time-steps is probably

the best choice as output file sizes become unwieldy otherwise. 

When run with monthly time steps, SWAT sums mass loadings over the course of each month

and averages concentrations over the course of each month. In the case of summed mass

loadings, AQUATOX divides the total loading by the days in the month to get an average daily

loading. Then, in order to prevent interpolation between data-points, AQUATOX loads these

values as data points at the beginning and the end of each month. This creates some “stairstepping” of input data into AQUATOX, but presents the best accounting for mass and

concentration data as provided by SWAT.

While the SWAT model can track several pesticides over land within a simulation, it only tracks

the movement of a single pesticide through the main channel. This means only a single pesticide

may be passed from SWAT to AQUATOX at a given time. The choice of which pesticide to

move into the main channel can be seen under the “Routing Pesticide” header within the screen

shown above. If the user wishes to track a specific pesticide from SWAT within AQUATOX, it

must be selected within this dialog box. 

Because AQUATOX only models organic chemicals, the linkage assumes that any pesticide data

passed to AQUATOX is in the form of an organic chemical. The user will later be asked to

specify the organic chemical being modeled from a list of available chemicals, or will be

required to input chemical-specific data about the organic chemical utilized.

Finally, a user may select to have “Stream Water Quality Processes” be “active” or “not-active”

within a SWAT simulation. Within SWAT, nutrient transformations in the stream are controlled

by the in-stream water quality component of the model. Even if active nutrient transformations

within the stream are not utilized, SWAT still calculates the movement of nutrients through the

system due to inflow loadings, and loadings from point and non-point sources. More

information about SWAT’s modeling of nutrients within a stream may be found in Chapter 25 of

the SWAT user’s manual (swat2000.PDF, located in the BASINS\DOCS\SWAT directory). 

Nutrients that can be modeled within SWAT include Ammonia, Nitrate, Phosphate, Oxygen, and

Biochemical Oxygen Demand. As AQUATOX also models each of these nutrient

compartments, these variables can be linked directly into AQUATOX from SWAT. Total

suspended solids (TSS) may also be linked from SWAT to AQUATOX.

In-stream water-quality processes modeled by SWAT within the sub-basin that is linked to

AQUATOX will not affect the AQUATOX simulation. AQUATOX only reads the inflow

loadings of nutrients within a particular SWAT reach and calculates in-stream water-quality

processes within its own derivatives. However, in-stream water-quality processes that occur
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upstream of the AQUATOX reach will affect the loadings of nutrients into AQUATOX, so the

user may still wish to utilize this option within SWAT. 

Important Note: By using a text file editor and editing the SWAT Input Control Code file

(*.COD file) a user may select to limit the number of variables that are output in a SWAT reach

file (*.RCH file). As the SWAT-AQUATOX linkage requires most of the variables from a

SWAT reach file to be present, the linkage will not work properly when the RCH files are

limited in this manner. 

4.3 Loading SWAT data into AQUATOX

To load SWAT data into AQUATOX, a user must first start AQUATOX. This can be done in

two ways. The user can run AQUATOX directly from the BASINS 3.0 menu by selecting

“AQUATOX” from the “Models” menu within the BASINS view:
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The user will then be asked whether she\he wishes to “Open AQUATOX with Linked BASINS

Stream data.” Selecting “No” indicates to the BASINS interface that the user is not trying to link

GIS data to AQUATOX. AQUATOX will then be started with no attached data.

If a user has already run the SWAT model and does not need to have BASINS open, the user can

run AQUATOX directly from the “Start” menu.

Once AQUATOX has started, a user can load SWAT data into AQUATOX by clicking on the

“Import Data from SWAT” button in the toolbar.

Alternatively, a user may select the “Import Data from SWAT” option from the “File” menu at

the upper left of the screen.
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Next, a dialog box appears asking the user to select the completed SWAT simulation from which

to import data. The user must select the “Control Input\Output File” (File.CIO) that is

associated with the SWAT simulation that is to be linked. This file will be found in the

“txtinout” directory under the directory named after your SWAT project. The full directory

structure will look as follows:

“BASINS\MODELOUT\SWAT\{your_project_name}\TXTINOUT\FILE.CIO”

The user will then see the following dialog box:

All sub-basins that are included in the SWAT simulation will be shown within the pull-down

interface. The user should select the relevant sub-basin to be linked to AQUATOX. The

resulting AQUATOX water body will correspond to the main channel within this sub-basin.

4.4 The Linkage Process

As with all BASINS-AQUATOX linkages, a user may choose to link SWAT parameters to a

“blank” AQUATOX simulation or overwrite relevant parameters and loadings in an existing

AQUATOX simulation. See Section 2.5 for more information about this choice.

AQUATOX models organic matter in four compartments:

• Labile Dissolved Organic Matter

• Labile Particulate Organic Matter

• Refractory Dissolved Organic Matter

• Refractory Particulate Organic Matter
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Within SWAT, BOD data is not broken down into these compartments. For this reason, a user

must specify the percentage of BOD that is Refractory and the percentage of BOD that is

Particulate organic matter. Default values are provided within the AQUATOX dialog box as

shown, and these values should be used if the user has no additional information about the BOD

loading.

The user will then be prompted as to whether a pesticide is tracked within the SWAT reach. If

the user selects “yes,” the loadings of the “Routing Pesticide” specified above will be linked into

the AQUATOX simulation. To model an organic toxicant within AQUATOX, parameters are

required about the chemical properties and toxicity of the substance. After selecting to model

the routing pesticide, the user will be prompted to load these chemical parameters from a

database of organic toxicants. Alternatively, the user can press “cancel” and enter these

chemical parameters later, within the AQUATOX “chemical underlying data” interface.
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From the SWAT linkage, AQUATOX will load data about channel geometry, nutrient and

pesticide loadings, simulation period, water flow, and organic and inorganic sediment loadings. 

In each case when a parameter value or time-series is loaded, AQUATOX writes the source and

result of the linkage into the log file. The log file can be viewed by pressing the “View Log

File” button from the screen shown below.
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From this screen, the user may continue to the AQUATOX Wizard to complete setting up the

new AQUATOX simulation or may bypass this step and work with AQUATOX through the

main AQUATOX interface. 

The data required to finish specifying a SWAT simulation are almost identical to those required

after an HSPF to AQUATOX linkage. The only difference is that water temperature is available

from an HSPF simulation but must be specified after a SWAT to AQUATOX linkage. For more

information about finishing the specification of the AQUATOX simulation, please see sections

2.7 and 2.8 (“Specification of Additional State Variables and Loadings” and “Run AQUATOX

and Plot Results”) in the “WINHSPF to AQUATOX Linkage”chapter . 
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5 AQUATOX TO GENSCN LINKAGE

5.1 Introduction

After an AQUATOX simulation has been run, a user may view output data using AQUATOX’s

output screens, a user may export the data to several database and spreadsheet formats, or the

user may choose to send the output data to GenScn, the post-processor within BASINS. GenScn

offers several statistical functions that are not available through the AQUATOX output screen

such as comparison of predicted and observed time-series and duration analysis.

5.2 Linking to GenScn

There are three ways to link to GenScn from within AQUATOX. 

1. Select “Export to GenScn” from the “File” menu.

2. Click the Export to GenScn button in the toolbar as shown here: .

3. Click the “Export All Results to GenScn” button on the Export Results Dialog.

All three of these options are enabled when AQUATOX has run a simulation and has results in

memory. These options are not enabled if GenScn has not been installed on a user’s computer.

When AQUATOX exports data to GenScn, a set of two files are written to the AQUATOX

“OUTPUT” directory. (This is the “OUTPUT” sub-directory within the directory in which

AQUATOX was installed). A file with an“RDB” extension is written that contains all of the

AQUATOX time-series results (control and perturbed), and a file with an “STA” extension is

written that tells GenScn the format and location of the RDB file. 

5.3 Using GenScn

The AQUATOX linkage produces a set of GenScn data within a single “Location” (the

AQUATOX river reach). There are up to two “Scenarios” produced, “Control” and “Perturbed,”

depending on which types of AQUATOX runs have been executed. (The “OBSERVED”

scenario that appears within GenScn is empty and should be ignored.) Finally, each AQUATOX

output variable is available under the GenScn “constituent” menu.

To produce a graph, a user can select the location, scenario, and constituent to graph and then

press the plus button at the top of the “Time Series” list. The constituent will appear as a new

item on the “Time Series” list. With this item selected, the user can then click on the “Generate

Graphs” button at the bottom of the screen and a graph generation dialog is created.
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For more information about how to use GenScn see GenScn.pdf located in the

BASINS\DOCS\GENSCN directory.