Methods, Models, Tools, and Databases for Water Research


  • Bacteria Methods
  • Biological Methods and Manual Development
    EPA's research in stream and source monitoring indicators includes fish, macroinvertebrates, periphyton, zooplankton, functional ecosystem indicators, water and sediment toxicity, and fish tissue contaminants. EPA exposure scientists regularly prepare and update field and laboratory protocol and methods manuals. They also provide technical assistance to EPA regions, program offices and states on the implementation and interpretation of these manuals. This website lists currently available manuals and protocols.
  • Coliphage Methods
  • Drinking Water Methods
  • Protozoan Methods
  • Regional Vulnerability Assessment (ReVA)
    EPA's ReVA program is an approach to regional scale, priority-setting assessment by integrating research on human and environmental health, ecorestoration, landscape analysis, regional exposure and process modeling, problem formulation, and ecological risk guidelines.
  • Virus Methods
    (EPA Manual of Methods for Virology) Twelve chapters. The individual chapters were prepared as ASCII text files to be viewed/printed with a monospaced font. It is planned to make them also available in PDF format in the future. The manual (EPA 600-4-84-013) describes in detail procedures for detecting viruses in environmental samples. 


  • Better Assessment Science Integrating point & Non-point Sources (BASINS)
    BASINS is a multi-purpose environmental analysis system that integrates a geographical information system (GIS), national watershed data, and state-of-the-art environmental assessment and modeling tools into one convenient package.
  • Bioaccumulation in Aquatic Systems Simulator (BASS)
    BASS is a model that simulates population and bioaccumulation dynamics of age-structured fish communities. While BASS was designed to investigate bioaccumulation of chemicals within community or ecosystem contexts, it also allows EPA to evaluate various dimensions of fish health associated with non-chemical stressors. Accurate bioaccumulation estimates help predict realistic dietary exposures to humans and fish-eating wildlife.
  • BIOCHLOR, Natural Attenuation Decision Support System
    BIOCHLOR is an easy-to-use screening model that simulates remediation by natural attenuation (RNA) of dissolved solvents at chlorinated solvent release sites. The software, programmed in the Microsoft Excel spreadsheet environment and based on the Domenico analytical solute transport model, has the ability to simulate 1-D advection, 3-D dispersion, linear adsorption, and biotransformation via reductive dechlorination (the dominant biotransformation process at most chlorinated solvent sites). Reductive dechlorination is assumed to occur under anaerobic conditions and dissolved solvent degradation is assumed to follow a sequential first-order decay process. BIOCHLOR includes three different model types:
    1. Solute transport without decay,
    2. Solute transport with biotransformation modeled as a sequential first-order decay process,
    3. Solute transport with biotransformation modeled as a sequential first-order decay process with two different reaction zones (i.e., each zone has a different set of rate coefficient values).
  • BIOPLUME II, Computer Model of Two-Dimensional Contaminant Transport under the Influence of Oxygen Limited Biodegradation in Ground Water
    BIOPLUME II is a simulation that computes concentrations of dissolved hydrocarbon under the influence of oxygen-limited biodegradation in an aquifer. The model solves the solute transport equation for both hydrocarbon and oxygen, assumes an instantaneous reaction between oxygen and hydrocarbon, and combines the two plumes using the principle of superposition. Computations account for convection, dispersion, mixing, and biodegradation effects. Also, the program can simulate slow hydrocarbon plumes undergoing biodegradation and can simulate in situ biorestoration schemes such as the injection of oxygenated water. Moreover, the model can simulate re-aeration and anaerobic biodegradation as a first-order decay in hydrocarbon concentrations.
  • BIOPLUME III, Natural Attenuation Decision Support System
    The BIOPLUME III program is a two-dimensional, finite difference model for simulating the natural attenuation of organic contaminants in ground water due to the processes of advection, dispersion, sorption, and biodegradation. The model simulates the biodegradation of organic contaminants using a number of aerobic and anaerobic electron acceptors: oxygen, nitrate, iron (III), sulfate, and carbon dioxide.
  • BIOSCREEN, Natural Attenuation Decision Support System
    BIOSCREEN is an easy-to-use screening model which simulates remediation through natural attenuation (RNA) of dissolved hydrocarbons at petroleum fuel release sites. The software, programmed in the Microsoft™ Excel spreadsheet environment and based on the Domenico analytical solute transport model, has the ability to simulate advection, dispersion, adsorption, and aerobic decay as well as anaerobic reactions that have been shown to be the dominant biodegradation processes at many petroleum release sites. BIOSCREEN includes three different model types:
    1. Solute transport without decay,
    2. Solute transport with biodegradation modeled as a first-order decay process (simple, lumped-parameter approach),
    3. 3) Solute transport with biodegradation modeled as an "instantaneous" biodegradation reaction (approach used by BIOPLUME models).
  • Capture Zone Analytic Element Model (CZAEM)
    CZAEM is a single-layer model for simulating steady flow in homogeneous aquifers using the Analytic Element Method. It serves as a tool in the wellhead protection decision making process by delineating groundwater capture zones and isochrones of residence times. CZAEM supports a limited number of analytic elements that can accommodate fairly realistic boundary conditions, such as streams, lakes, and aquifer recharge due to precipitation. CZAEM generates output on groundwater capture zones and residence times. The model accurately defines capture zone boundaries by first determining all stagnation points and dividing streamlines in the flow domain.
  • Environmental Fluid Dynamics Code (EFDC)
    EFDC is a state-of-the-art hydrodynamic model that can be used to simulate aquatic systems in one, two, and three dimensions. It is a multifunctional surface water modeling system, which includes hydrodynamic, sediment-contaminant, and eutrophication components.
    EPANET is software that models water distribution piping systems. It performs extended-period simulation of the hydraulic and water quality behavior within pressurized pipe networks.
  • Exposure Analysis Modeling System (EXAMS)
    EXAMS is an interactive software application for formulating aquatic ecosystem models and rapidly evaluating the fate, transport, and exposure concentrations of synthetic organic chemicals including pesticides, industrial materials, and leachates from disposal sites.
    FOOTPRINT simulates the length and surface area of BTEX plumes in groundwater, when the plumes are produced from a gasoline spill that contains ethanol.
  • Hydrocarbon Spill Screening Model (HSSM)
    Hydrocarbon Spill Screening Model (HSSM), simulates flow of the light nonaqueous-phase liquid (LNAPL) transport of a chemical constituent of the LNAPL from the surface to the water table, radial spreading of the LNAPL at the water table, and dissolution and aquifer transport of the chemical constituent. The HSSM model is one-dimensional in the vadose zone, radial in the capillary fringe, and two-dimensional in the vertically averaged analytical solution of the advection dispersion equation in the saturated zone. The model is based on the KOPT, OILENS and TSGPLUME models.
    1. HSSM-DOS
    2. HSSM-Windows
    3. HSSM en Español
  • Infiltration Models
    The unsaturated or vadose zone provides a complex system for the simulation of water movement and contaminant transport and fate. Numerous models are available for performing simulations related to the movement of water. There exists extensive documentation of these models. However, the practical application of these infiltration models has not been adequately addressed in the literature. In recent years, the use of vadose zone models has increased for the purpose of estimating contaminant levels in soils related to different types of remedial decision-making. The rate of infiltration of water is generally the most important parameter required in such models. Often these models use an over-simplified estimate of the infiltration rate, which has little basis in reality and actual field conditions. This site presents a compilation of simple infiltration models for quantifying the rate of water movement. A great majority of the compiled models are based on widely-accepted concepts of soil physics. These models, represented by simple mathematical expressions, can be readily implemented in a spreadsheet environment. Proper use of these models should provide a rational and scientific basis for remedial decision-making related to soil contaminant levels.
    MINTEQA2 is a equilibrium speciation model that can be used to calculate the equilibrium composition of dilute aqueous solutions in the laboratory or in natural aqueous systems. The model is useful for calculating the equilibrium mass distribution among dissolved species, adsorbed species, and multiple solid phases under a variety of conditions including a gas phase with constant partial pressures.
  • MOFAT: A Two-Dimensional Finite Element Program for Multiphase Flow and Multicomponent Transport
    MOFAT is a two-dimensional, finite element model for simulating coupled multiphase flow and multi-component transport in planar or radically symmetric vertical sections. MOFAT evaluates flow and transport for water, nonaqueous-phase liquid (NAPL), and gas. The program also can be used when gas or NAPL phases are absent in part or from all of the domain. The flow module can analyze two-phase flow of water and NAPL in a system of constant gas pressure, or explicit three phase flow of water. The transport module can accommodate up to five components, partitioning among water, NAPL, gas, and solid phases, assuming local equilibrium inter-phase mass transfer or first-order kinetically controlled mass transfer.
  • Nonaqueous Phase Liquid (NAPL) Simulator
    This model simulates the contamination of soils and aquifers that results from the release of organic liquids, commonly referred to as nonaqueous-phase liquids (NAPLs). The simulator is applicable to three interrelated zones: a vadose zone that is in contact with the atmosphere, a capillary zone, and a water-table aquifer zone. Three mobile phases are accommodated: water, NAPL, and gas. The three-phase k-S-P sub-model accommodates capillary and fluid entrapment hysteresis. NAPL dissolution and volatilization are accounted for through rate-limited mass transfer sub-models.
  • Optimal Well Locator (OWL)
    This model evaluates existing monitoring well networks and optimizes the selection of new monitoring well locations.
  • Pesticide Analytical (PESTAN) Model
    PESTAN is used to estimate the vertical migration of dissolved organic solutes through the vadose zone to groundwater. Estimates are based on a closed-form analytical solution of the advective-dispersive-reactive transport equation. The model is intended for use in conducting initial screening assessments of the potential for contamination of ground-water from currently registered pesticides and those submitted for registration.
  • Remediation Evaluation Model for Chlorinated Solvents (REMChlor)
    This model simulates the transient effects of groundwater source and plume remediation. This is a contaminant source model based on a power-function relationship between source, mass, and discharge. It can consider partial source remediation at any time after release. The source model is a time-dependent, mass-flux boundary condition to the analytical plume model (one-dimensional flow), which simulates first-order sequential decay and production of several species. This model also calculates cancer risks posed by carcinogenic species.
  • Remediation Evaluation Model for Fuel Hydrocarbons (REMFuel)
    An analytical solution for simulating the transient effects of groundwater source and plume remediation for fuel hydrocarbons. In the analytical method, the contaminant source model is based on a power function relationship between source mass and source discharge for multiple fuel constituents, and it can consider partial source remediation at any time after the initial release. The source model serves as a time-dependent mass flux boundary condition to the analytical plume model, where flow is assumed to be one dimensional. The plume model for each fuel component simulates first order sequential decay and production of one daughter species. REMFuel can also simulate zero order or Monod's kinetics for decay of fuel components in the plume. The decay rates and other reaction coefficients are variable functions of time and distance in the plume. This approach allows for flexible simulation of enhanced plume remediation that may be temporary in time, limited in space, and which may have different effects on different contaminant species in the plume.
  • ReVA
    EPA's Regional Vulnerability Assessment (ReVA) program is an approach to regional scale, priority-setting assessment by integrating research on human and environmental health, ecorestoration, landscape analysis, regional exposure and process modeling, problem formulation, and ecological risk guidelines.
  • Regulatory and Investigative Treatment Zone (RITZ) Model
    RITZ is a screening model for simulation of unsaturated zone flow and transport of oily wastes during land treatment. RITZ was developed to help decision makers systematically estimate the movement and fate of hazardous chemicals during land treatment of oily wastes. The model considers the downward movement of the pollutant with the soil solution, volatilization, and loss to the atmosphere and degradation. The model incorporates the influence of oil upon the transport and fate of the pollutant.
  • River and Stream Water Quality Model (QUAL2K)
  • QUAL2K (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).
  • Storm Water Management Model (SWMM)
    This general purpose urban hydrology and conveyance system hydraulics software is a dynamic rainfall-runoff simulation model used for single event or long-term (continuous) simulation of runoff quantity and quality from primarily urban areas.
  • Two-Dimensional Subsurface Flow, Fate and Transport of Microbes and Chemicals (2DFATMIC)
    This model simulates subsurface flow, fate, and transport of contaminants that are undergoing chemical or biological transformations. This model is applicable to transient conditions in both saturated and unsaturated zones.
  • Three-Dimensional Subsurface Flow, Fate and Transport of Microbes and Chemicals (3DFATMIC)
    3DFATMIC uses a Lagrangian-Eulerian adapted zooming and peak capturing (LEZOOMPC) algorithm. This 3-dimensional model can completely eliminate peak clipping, spurious oscillation, and numerical diffusion; i.e., solve the advective transport problems exactly, within any prescribed error tolerance, using very large mesh Courant numbers. The size of mesh Courant number is limited only by the accuracy requirement of the Eulerian step. Since this model also includes diffusion zooming in solving diffusion elemental matrix, the accuracy is improved by specifying the number of local subelements in every global element. In other words, the more subelements zoomed in diffusion step, the more accuracy at Eulerian step. To sum up, a better solution with respect to advection transport can be obtained with larger time-step sizes; the time-step sizes are only limited by the accuracy requirement with respect to diffusion/dispersion transport and chemical reaction terms. However, the limitation of time-step size imposed by diffusion/dispersion transport is normally not a very severe restriction.
  • Virulo
    Virulo is a probabilistic screening model for predicting leaching of viruses in unsaturated soils. Monte Carlo is employed to generate ensemble simulations of virus attenuation. The probability of failure is generated to achieve a user-chosen degree of attenuation.
    VLEACH is a one-dimensional, finite difference model for making preliminary assessments of the effects on groundwater from the leaching of volatile, sorbed contaminants through the vadose zone. The program models four main processes: liquid-phase advection, solid-phase sorption, vapor-phase diffusion, and three-phase equilibration.
  • WhAEM
    This program delineates capture zones and isochrones of groundwater residence time for the purpose of wellhead protection. Processes include steady state, homogeneous, isotropic, advection, and dispersion.

Top of Page


  • CHEMFLO™-2000, Interactive Software for Simulating Water and Chemical Movement in Unsaturated Soils
    CHEMFLO-2000 enables users to simulate water movement and chemical fate and transport in vadose zones. The software can be used to assist regulators, environmental managers, consultants, scientists, and students in understanding unsaturated flow and transport processes. Water movement and chemical transport are modeled using the Richards and the convection-dispersion equations, respectively. The equations are solved numerically using the finite differences approach.
  • Geostatistical Environmental Assessment (GEOEAS)
    GEOEAS is a collection of interactive software tools for performing two-dimensional geostatistical analyses of spatially distributed data. The principal function of the package is the production of grids and contour maps of interpolated (kriged) estimates from sample data. GEOEAS can produce data maps, univariate statistics, scatter plots/linear regression, and variogram computation and model fitting.
  • Geostatistical Software Package (GEOPACK)
    GEOPACK is a comprehensive geostatistical software package that allows both novice and advanced users to undertake geostatistical analyses of spatially correlated data. The program:
    1. Generates graphics (for example, linear or logarithmic line plots, and contour and block diagrams)
    2. Computes basic statistics (for example, mean, median, variance, standard deviation, skew, and kurtosis)
    3. Runs programs for linear regression, polynomial regression, and Kolomogorov-Smirnov tests
    4. Calculates linear estimations and nonlinear estimations
    5. Determines sample semivariograms and cross semivariograms
    GEOPACK allows users to incorporate additional programs at a later date without having to alter previous programs or recompile the entire system.
  • HSPF Toolkit for BMP Modeling Applications (FTABLE)
  • The Hydrological Simulation Program - FORTRAN (HSPF) Toolkit is a comprehensive package for simulation of watershed hydrology and water quality for both conventional and toxic organic pollutants. HSPF incorporates watershed-scale agricultural runoff management models and nonpoint source models into a basin-scale analysis framework that includes fate and transport in one dimensional stream channels. It is the only comprehensive model of watershed hydrology and water quality that allows integrated simulation of land and soil contaminant runoff processes with in-stream hydraulic and sediment-chemical interactions.
  • ReVA Data
    ReVA uses EPA's Environmental Information Management System (EIMS) to manage its library of projects, data sets, models, and documents. The EIMS database is a comprehensive resource for persons interested in environmental information. By accessing EIMS, you will be able to browse and review ReVA's current data, meetings, projects, and documents.
  • ReVA Tools and Projects 
    EPA's Regional Vulnerability Assessment (ReVA) program is designed to create the methods needed to understand a region's environmental quality and its spatial pattern. Impacts of human activities are not uniformly distributed across landscapes and regions (defined here as a multi-state area) and are often interacting in complex ways.
  • ReVA - Environmental Decision Toolkits under development
  • Stormwater Calculator
    The National Stormwater Calculator, a part of President Obama’s Climate Change Action Plan, is a desktop application that estimates the annual amount of stormwater runoff from a specific location in the United States (including Puerto Rico). Estimates are based on local soil conditions, land cover and historic rainfall records. The Calculator also includes changes in seasonal precipitation levels, the effects of more frequent high-intensity storms, and changes in evaporation rates based on validated Intergovernmental Panel on Climate Change climate vulnerability scenarios.
  • Supercomputer for Model Uncertainty and Sensitivity Evaluation (SuperMUSE)
    EPA’s Supercomputer for Model Uncertainty and Sensitivity Evaluation, or SuperMUSE, enhances quality assurance in environmental models and applications. Uncertainty analysis (UA) and sensitivity analysis (SA) remain critical, though often overlooked steps in the development and evaluation of computer models. As a result of the SuperMUSE hardware and software technology, EPA can now better investigate new and existing UA and SA methods. EPA can also more easily achieve UA/SA of complex, Windows-based environmental models, allowing scientists to conduct analyses that have, to date, been impractical to consider.
    SUSTAIN is a decision support system to facilitate selection and placement of Best Management Practices (BMPs) and Low Impact Development (LID) techniques at strategic locations in urban watersheds. It was developed to assist stormwater management professionals in developing implementation plans for flow and pollution control to protect source waters and meet water quality goals. From an understanding of the needs of the user community, SUSTAIN was designed for use by watershed and stormwater practitioners to develop, evaluate, and select optimal BMP combinations at various watershed scales on the basis of cost and effectiveness. SUSTAIN is a tool for answering the following questions:
    • How effective are BMPs in reducing runoff and pollutant loadings?
    • What are the most cost-effective solutions for meeting water quality and quantity objectives?
    • Where, what type of, and how big should BMPs be?
    The SSOAP toolbox is a suite of computer software tools used for the quantification of RDII and help capacity analysis and condition assessment of sanitary sewer systems. This toolbox includes EPA’s Storm Water Management Model Version 5 (SWMM5) for performing dynamic routing of flows through the sanitary sewer systems.
  • Retention Curve (RETC) Computer Program
    RETC is a program for analyzing the hydraulic conductivity properties of unsaturated soils. The parametric models of Brooks-Corey and van Genuchten are used to represent the soil water retention curve. The theoretical pore-size distribution models of Mualem and Burdine predict the unsaturated hydraulic conductivity function. The simulation can be generated from observed soil water retention data, assuming that one observed conductivity value (not necessarily at saturation) is available. The program also permits users to fit analytical functions simultaneously to observed water retention and hydraulic conductivity data.
  • Ubertool: Ecological Risk Web Application for Pesticide Modeling
    EPA scientists have developed a prototype cloud computing-base knowledge management system to support ecological risk decisions mandated under the Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA) and the Endangered Species Act.  The “Ubertool” dashboard infrastructure integrates the processing of model results for over a dozen commonly-used EPA aquatic and terrestrial regulatory models and supporting datasets.
  • Virtual Beach (VB)
    When recreational waters are contaminated by bacteria and other microorganisms, beach managers need to act quickly to protect public health. EPA scientists developed Virtual Beach, a software suite that uses data on beach location, local hydrology, land use, wave height, and weather to create models that can predict bacteria and other waterborne pathogen outbreaks at saltwater and freshwater beaches before they happen. Using Virtual Beach, beach managers can issue same-day beach closures or health advisories to protect the health of swimmers and the surrounding community.
  • Watershed Health Assessment Tools Investigating Fisheries (WHATIF)
    WHATIF is software that integrates a number of calculators, tools, and models for assessing the health of watersheds and streams with an emphasis on fish communities in the Mid-Atlantic Highland region.

Top of Page


  • Drinking Water Treatability Database
    The Drinking Water Treatability Database presents referenced information on the control of contaminants in drinking water. It allows drinking water utilities, first responders to spills or emergencies, treatment process designers, research organizations, academicians, regulators and others to access referenced information gathered from thousands of literature sources and assembled on one site.
  • Environmental Geophysics
    This website beta version contains information on geophysical methods, references to geophysical citations, and a glossary of geophysical terms related to environmental applications.
  • HELP
    A quasi-two-dimensional modeling program that simulates water movement into and out of landfills based on a waste management system=s particular design. The user can conduct water-balance analyses of solid waste disposal and containment facilities.
  • Landscape Ecology Data Browsers
    A one-dimensional, steady-state model used to predict the concentration of contaminants migrating from a waste disposal facility via the subsurface, surface water, and air pathways to receptor sites.
  • PPCP (Reference Databases)
    Published Literature Relevant to the Issues Surrounding PPCPs as Environmental Contaminants
  • ReVA Data
    ReVA uses EPA's Environmental Information Management System (EIMS) to manage its library of projects, data sets, models, and documents. The EIMS database is a comprehensive resource for persons interested in environmental information. By accessing EIMS, you will be able to browse and review ReVA's current data, meetings, projects, and documents.
  • ReVA - Environmental Decision Toolkits under development
  • Virtual Field Reference Data Base VFRDB
    The Neuse River Basin VFRDB provides in situ reference measurement data for statistically rigorous accuracy assessments of land-cover maps derived from satellite and airborne remote sensing platforms.
    A one-dimensional, finite difference model for making preliminary assessments of the effects on ground water from the leaching of volatile, sorbed contaminants through the vadose zone. The program models four main processes: liquid-phase advection, solid-phase sorption, vapor-phase diffusion, and three-phase equilibration.
  • Watershed Deposition Tool Data
  • WhAEM2000
    WhAEM2000 is a public domain and open source general purpose ground-water flow modeling system, with strengths in representing regional flow systems, and ground water/surface water interactions. Read the WhAEM Abstract.
  • WHPA
    A semi-analytical ground-water flow simulation program used for delineating capture zones in a wellhead protection area. The program consists of four computational modules (RESSQC, MWCAP, GPTRAC, MONTEC).