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Environmental Modeling Community of Practice

What's New in AQUATOX Release 3.2?

AQUATOX Release 3.2

AQUATOX 3.2 Fact Sheet  September 2018

AQUATOX 3.2 includes the following interface enhancements:

  • Update to AQUATOX Database Management System:  The paradox database management system (used in previous versions) has been replaced with SQLite databases.   
  • Capability to save all inputs and outputs to a text file:  AQUATOX now can write all model inputs and outputs in ASCII format by saving files with a “*.txt” extension.  This allows users to view and change model inputs without using the graphical user interface.
  • Command Line Version:  Users may now execute and manipulate the model using a DOS command prompt.  
  • For information about how to use each of these interface updates, please see the Release 3.2 User’s Manual.

In addition to the changes discussed above, changes were made to the model to represent the “nearshore marine environment” as discussed here.

Nearshore Marine Environment

AQUATOX Release 3.2 was designed to extend the existing AQUATOX estuarine version to include improved capabilities for situations encountered in the nearshore marine environment. Several changes were required to model food webs in the marine environment.  The most notable updates include:

  • Additional equations to model the physical complexity of oyster reefs and the marsh-edge environment.
  • The capability to model size-classes of oysters and crabs within the model.
  • New invertebrate-modeling capabilities including allometric bioenergetics equations and burrowing refuge from predation.  
  • To better represent marine-biology conventions, the guilds used by AQUATOX to characterize these state variables were reorganized.
  • Four new nearshore-marine studies are included in this version representing “marsh edge,” “exposed beach,” “soft bottom,” and “oyster reef” habitats.  Numerous nearshore-marine animal- and plant-parameter records have been added to the AQUATOX databases.

Differences from Release 3.1 plus


Most model simulations created in Release 3.1 and Release 3.1 plus produce identical or nearly-identical results in Release 3.2.  A few differences are visible in some studies, however.  Nutrient quantities may be slightly different because of a change in the animal-respiration equation.  This can have some ripple effects, especially in systems with long retention times.  Other changes to the process code that could affect model results follow:

  • The BCF equation (382) has been changed to take into account metabolism of organic chemicals.  
  • A bug was fixed when the user has selected the “Calculate BCF” option (alternative chemical uptake mode given a user entered “K1” and “K2”).  
  • Carrying capacity was not utilized as a parameter for benthic invertebrates previously, but now is considered a hard cap based on habitat limitations.
  • For full details about these changes please see the AQUATOX Release 3.2 Technical Documentation.

AQUATOX Release 3.1 Plus

AQUATOX 3.1 Fact Sheet  (EPA-820-F-12-023) August 2012

AQUATOX Release 3.1 Plus includes the following enhancements:

  • Option to model nutrient limitation in plants based on internal rather than external nutrients.  This allows for luxury uptake of nutrients during high-nutrient periods and expenditure of nutrient stores during lower-nutrient periods.  Concentrations and derivative rates may be output from these new internal-nutrient state variables as well as the nutrient-to-organism ratio for each plant.  This option should improve the prediction of the timing and duration of algal blooms.       
  • Sinking of plants and suspended detritus is now affected by the salinity & therefore the density of water in non-estuary segments.
  • New outputs for net primary productivity, pelagic invertebrate biomass, benthic invertebrate biomass, and fish biomass.     
  • Capability to load and save observed data to a file to move from one study to another.      
  • Significantly optimized loading and saving of very large aps or als files.
  • For moving water (streams and rivers), the average water temperature must drop below 0 deg. C before ice cover is assumed.

AQUATOX Release 3.1

AQUATOX Release 3.1 includes numerous significant enhancements over previous versions that increase the realism and utility of the model. The most important enhancements include:

  • Addition of sediment-diagenesis "steady-state" mode to significantly increase model speed;
  • Modification of denitrification code in order to simplify calibration and to achieve alignment with other models;
  • Enabled importation of equilibrium CO2 concentrations to enable linkage to CO2SYS and similar models;
  • New BOD to organic matter conversion relying on percent-refractory detritus input; input and output BOD is clarified to be "carbonaceous" BOD.
  • Refinements for floating plants:
    • Added floating option for plants other than cyanobacteria (formerly labeled "blue-green algae”)
    • Converted the averaging depth for floating plants to the top three meters to more closely correspond to monitoring data
    • Floating plants now explicitly move from the hypolimnion to the epilimnion when a system is stratified.
  • Modifications to PFA (perfluoroalkylated surfactants) model to increase flexibility:
    • Uptake rates (K1s) and elimination rates (K2s) are visible and editable for animals and plants
    • New interface to estimate animal K1s and K2s as a function of chain length
    • Improved gill-uptake equation for invertebrates.
  • Bioaccumulation and toxicity modeling improvements:
    • Optional alternative elimination-rate estimation for animals based on Barber (2003) ; works best with PCBs;
    • Updated ICE (toxicity regressions), based on new EPA models released in February 2010 and improved AQUATOX ICE interface;
    • Addition of output of K1, K2, and BCF estimates.
  • Improved sensitivity and uncertainty analyses:
    • "Output to CSV" option for uncertainty runs so that complete results for every iteration may be saved and examined;
    • Option for non-random sampling for "statistical sensitivity analyses";
    • A "reverse tornado" diagram (effects diagram) that shows the effects of each parameter change on the overall simulation;
    • Nominal range sensitivity analysis has been added for linked- segment applications.
  • Database Improvements:
    • AQUATOX database search functions dramatically improved;
    • "Scientific Name" field added to Animal and Plant databases.
  • Interface and Data Input Improvements:
    • Software and software installer is 64-bit OS compatible;
    • Added an option in the "Setup" screen to trigger nitrogen fixation based on the N to P ratio;
    • Addition of output variables to clarify whether photosynthesis is sub-optimal due to high-light or low-light conditions;
    • Time-varying evaporation option in the "Site" screen has linkage from the "Water Volume" screen;
    • Grid mode within a study so that all animal, plant, and chemical parameters in a study can be tabulated, examined, edited, and exported to Excel;
    • Added capability to input time-series loads of fish based on fish stocking;
    • Updated HSPF WDM file linkage to be more generally applicable (does not require use of WinHSPF, the version of HSPF contained in BASINS);
    • Enabled hourly loadings for the following variables: all nutrients, CO2, Oxygen, Inorganic suspended sediments (sand/silt/clay), TSS, Light, Organic Matter;
    • "Graph Setup" window now enabled for linked-mode graphics;
    • Other minor interface improvements.

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