U.S. EPA Contaminated Site Cleanup Information (CLU-IN)

U.S. Environmental Protection Agency
U.S. EPA Technology Innovation and Field Services Division


Risk Assessment


Sediment and Bioavailability

The Terminology Reference Section of the USEPA Web site defines bioavailability as "A measure of the physicochemical access that a toxicant has to the biological processes of an organism. The less the bioavailability of a toxicant, the less the toxic effect on the organism." This broad definition provides a foundation for understanding this complex topic, as it applies to organisms of varying complexity, from bacteria to human beings.

Incorporating Bioavailability Considerations into the Evaluation of Contaminated Sediment Sites
Interstate Technology & Regulatory Council (ITRC) Contaminated Sediments Team, Web-based resource, Feb 2011

This Web-based ITRC technical and regulatory guidance is intended to help state regulators and practitioners understand and incorporate bioavailability concepts in contaminated freshwater or marine sediment management practices. The website is constructed to help the user identify the most relevant places within an exposure assessment where bioavailability can be assessed using the tools and methods that are most appropriate. Case studies are provided.


The bioavailability of organic and inorganic contaminants in sediment is affected by bioturbation, a dynamic, biotic process that brings about the constant mixing of the top layer of sediment. Both plants and animals contribute to bioturbation, but usually benthic invertebrates, the annelid (segmented) worms, insect larvae, and bivalve mollusks, such as clams and mussels, are the major contributors to the process. As these animals construct galleries and burrow into sediment they can drag contaminated particles down from the sediment�s surface into the deeper layers. However, these actions can also bring contaminants in the deeper layers to the surface. Burrowing animals release fine, contaminant-containing fecal material to the surface of the sediment, where the contaminants may become bioavailable. The benthic invertebrates represent an important link between contaminated sediments and higher-tier receptors, such as waterfowl (Meysman 2006).

Adobe PDF LogoBioturbation: A Fresh Look at Darwin's Last Idea
Meysman, F.J., J.J. Middleburg, and C.H. Help.
Trends in Ecology and Evolution, Vol 21, No 12, p 688-695, 2006

This article on bioturbation contains general information on the role of bioturbation in sediments.


Sediments play a pivotal role in controlling the bioavailability of metallic and organic contaminants of concern. The release of bioavailable mercury from contaminated lake sediment provides one example. Sulfate reducing bacteria (SRB) are present in the surficial sediments and the anoxic (oxygen deprived) waters that immediately cover them. SRB in the first few centimeters of anoxic lake sediment convert mercury stored in the sediment to its most common organic form, methyl mercury (MeHg). MeHg�s high solubility and capacity to rapidly pass through cell membranes makes it readily bioavailable (USEPA 1997).

Although analysis of a particular sediment may indicate elevated concentrations of a toxic metal, or a mixture of toxic metals, this does not necessarily mean the metals are biologically available to benthic organisms. The geochemistry of a particular sediment governs the bioavailability of metals, such as cadmium, copper, lead, nickel, silver, and zinc. Generally, heavy metals are present as sulfide complexes in the deeper layers of sediment, and are minimally bioavailable due to their near-total insolubility. The oxidation state of a metal may affect its bioavailability. For example, the reduced form of the element chromium, chrome III (CrIII), is less readily available then the highly oxidized form, chromium VI (CrVI). Sediment geochemistry will determine the oxidation state of chromium and metals that have multiple valence states. (WHO 2006).

The concept of bioavailability is used to generate protective benchmark concentrations such as equilibrium partitioning sediment benchmarks (ESBs). An ESB is a point of reference concentration below which adverse effects to benthic organisms are not expected, and can be used by environmental managers to provide a level of protection for these organisms. However, if site-specific sediment contaminant levels exceed the benchmark, this should prompt a decision to gather additional data to further evaluate potential toxicity and bioavailability (USEPA 2005).

When considering the magnitude of toxic risk from the ingestion of contaminated sediment in a HHRA or ERA, the concept of bioavailability is important. In this instance, bioavailability refers to the fraction of the ingested amount of a contaminant that passes through the wall of the gut and becomes available for distribution to other parts of the body. The size of this fraction is therefore of great importance when determining the magnitude of the health risk from ingested, contaminated sediment (USEPA 2007).

Acid Volatile Sulfide and Simultaneously Extracted Metals in the Sediment Cores of the Pearl River Estuary in South China
Fang, T., X. Li, and G. Zhang.
Ecotoxicology and Environmental Safety, Vol 61, p 420-431, 2005 (abstract)

Appendix A: Adjustments for Absorption Efficiency
In Risk Assessment Guidance for Superfund (RAGS) Part A.
USEPA, Office of Solid Waste and Emergency Response, EPA 540/1-89/002, 4 pp, 1989

Bioavailability of Contaminants in Soils and Sediments: Processes, Tools and Applications
National Academy of Sciences, 432 pp, 2003

Adobe PDF LogoEnvironmental Health Criteria 234: Elemental Speciation in Human Health Risk Assessment
World Health Organization, 256 pp, 2006

Adobe PDF LogoGuidance for Evaluating the Oral Bioavailability of Metal in Soils for Use in Human Health Risk Assessment
USEPA, Office of Solid Waste and Emergency Response, OSWER Directive 9285.7-80, 20 pp, 2007

Adobe PDF LogoMercury Study Report to Congress, Volume III: Fate and Transport of Mercury in the Environment
USEPA, Office of Air Quality Planning and Standards and Office of Research and Development, EPA 452/R-97/005, 376 pp, 1997

Adobe PDF LogoMercury Study Report to Congress, Volume IV: An Assessment of Exposure to Mercury in the United States
USEPA, Office of Air Quality Planning and Standards and Office of Research and Development, EPA 452/R-97/006, 293 pp, 1997

Adobe PDF LogoProcedures for the Derivation of Equilibrium Partitioning Sediment Benchmarks (ESBs) for the Protection of Benthic Organisms: Metal Mixtures (Cadmium, Copper, Lead, Nickel, Silver and Zinc)
USEPA, Office of Research and Development, EPA 600/R-02/011, 121 pp, 2005

Organic Compounds

Sediments are frequently contaminated by organic pollutants, such as chlorinated pesticides, PCBs, PAHs, PCDDs, PCDFs, and petroleum derived fuel oils. The USEPA has published procedures (USEPA 2003) that derive ESBs for the two organochlorine pesticides, dieldrin and endrin, and for PAH mixtures. USEPA also has derived second tier (Tier 2) ESBs for 32 nonionic organic compounds (USEPA 2008). An ESB for an organic compound is not based on a relationship between relatively insoluble sulfide-complexed and a more readily soluble form. However, organic ESBs still employ the concept of partitioning between freely available and less bioavailable forms. An organic ESB assumes steady-state equilibrium between pore water, sediment, and benthic organism tissue concentrations. If one of these concentrations is known, the others can be calculated. An aqueous toxicity value (expressed as a concentration) can therefore be used to predict the toxicity of a compound in sediment. A non-polar organic ESB is obtained by multiplying an aqueous toxicity value (such as its Water Quality Criteria) for the compound with its organic carbon-water partition coefficient (KOC). Compounds with high KOC values partition to the organic carbon fraction of sediment and become less bioavailable to benthic organisms. Less rigorous inputs may be used to derive a Tier 2 ESB than for a Tier 1 ESB. For example, a secondary chronic toxicity value may be used for a Tier 2 ESB derivation, and the resulting value may have greater uncertainty.

Bioavailability of Organic Compounds: Methods and Case Studies
National Institutes of Health, National Institute of Environmental Health Sciences, Superfund Basic Research Program.

This is an audio and slide presentation on the bioavailability of PAHs from sediment.

Ecological Risk Assessment of Polycyclic Aromatic Hydrocarbons in Sediments: Identifying Sources and Ecological Hazard
Neff, J.N., S.A. Stout, and D.G. Gunster.
Integrated Environmental Assessment and Management, Vol 1, No 1, 2005 (abstract)

Estimation of Biota Sediment Accumulation Factor (BSAF) from Paired Observations of Chemical Concentrations in Biota and Sediment
Burkhard, L.
EPA 600-R-06-047, 35 pp, 2009

BSAF is a parameter describing bioaccumulation of sediment-associated organic compounds or metals into tissues of ecological receptors. The report provides information on methodologies to estimate BSAF for nonionic organic chemicals. It is applicable to fish and benthic organisms, e.g., crabs and bivalves.

Adobe PDF LogoEvaluating Ecological Risk to Invertebrate Receptors from PAHs in Sediments at Hazardous Waste Sites
Burgess, Robert M.
EPA, Office of Research and Development, EPA/600/R-06/162F, 23 pp, 2009

Adobe PDF LogoProcedures for the Derivation of Equilibrium Partitioning Sediment Benchmarks (ESBs) for the Protection of Benthic Organisms: Dieldrin
USEPA, Office of Research and Development, EPA 600/R-02/010, 75 pp, 2003

Adobe PDF LogoProcedures for the Derivation of Equilibrium Partitioning Sediment Benchmarks (ESBs) for the Protection of Benthic Organisms: Endrin
USEPA, Office of Research and Development, EPA 600-R-02-009, 73 pp, 2003

Adobe PDF LogoProcedures for the Derivation of Equilibrium Partitioning Sediment Benchmarks (ESBs) for the Protection of Benthic Organisms: PAH Mixtures
USEPA, Office of Research and Development, EPA 600/R-02/013, 175 pp, 2003

Adobe PDF LogoProcedures for the Derivation of Equilibrium Partitioning Sediment Benchmarks (ESBs) for the Protection of Benthic Organisms: Compendium of Tier 2 Values for Nonionic Organics
USEPA, Office of Research and Development, EPA 600/R-02/016, 75 pp, 2008

Metals Assessment Issue Paper: Bioavailability and Bioaccumulation
Lanno, R.P.
USEPA Bioavailability Workshop, 15-16 April 2003, 27 slides, PowerPoint presentation, 2003

Sediment and Bioaccumulation

The bioaccumulation of contaminants can be defined generally as the accumulation of organic compounds, such as chlorinated pesticides, PAHs, and PCBs, or heavy metals in an animal or plant. Bioaccumulation requires the sequestration of contaminants that enter the organism through diet, water intake, respiration, and skin or root contact, resulting in contaminant concentrations that are greater than those of the organism�s environment. In contrast, accumulation of a substance only through contact with water is known as bioconcentration. The contaminant concentration achieved by bioaccumulation is governed by many factors, such as rate of uptake, rate of elimination, metabolic transformation of the contaminant, lipid content of the organism, and integrity and health of the organism.

Contaminants in sediment represent a crucial first step toward passage into the food chain. The bioavailability of contaminants in surficial sediments and contaminants released into the pore water and water column by biotic and abiotic processes in the sediment layer provides an opportunity for bioaccumulation. Contaminants in bed sediments transfer to benthic organisms by direct contact with or ingestion of sediment particles and from sediment pore water. The relative contributions of these three pathways are difficult to predict. They vary with the particle size and composition of the sediment, the species of organism, and the physical chemistry of the contaminant. Once transferred to biota, contaminants may accumulate if no mechanism exists for their elimination. Non-ionic organic contaminants accumulate usually in the lipid-rich tissues of an organism. Some metals accumulate due to binding to protein. Bioaccumulated contaminants can exert toxic effects on the organism containing them and on the subsequent trophic levels that acquire them in prey.

As contaminants (MeHg, cadmium, PCBs, and chlorinated pesticides, such as DDT) move up the food chain from one trophic level to the next, biomagnification can occur. Biomagnification is the progressive accumulation of contaminants such that the concentration in a predator�s tissues exceeds the level in its prey by a large factor. Biomagnification occurs as a contaminant moves from one trophic level to the next higher level in the food chain. As successive trophic levels require greater amounts of prey, great increases in contaminant concentration can be seen (ATSDR Toxicological Profiles).

Toxicological Profiles
Agency for Toxic Substances and Disease Registry (ATSDR).

ATSDR publishes toxicological profiles for organic and inorganic chemicals. Information on the chemical�s bioaccumulation potential is given in each profile.

Adobe PDF LogoBioaccumulation Models: State of the Application at Large Superfund Sites
Gustavson, K., T. von Stackelberg, I. Linkov, and T. Bridges.
ERDC TN-DOER-R17, 31 pp, 2011

Food web bioaccumulation models are important in determining remedial actions as they often are used to establish sediment cleanup levels and compare the effect of various remedial scenarios on fish tissue concentrations. Model application can differ markedly from site to site owing to the absence of prescribed methods for selecting and applying the models to contaminated areas. This technical note reviews the application of bioaccumulation models at four large contaminated-sediment Superfund sites to document the state of the practice and to draw conclusions and recommendations from that combined experience.

Adobe PDF LogoBiological Processes Affecting Bioaccumulation, Transfer, and Toxicity of Metal Contaminants in Estuarine Sediments
Chen, C.Y., N.S. Fisher, and J.R. Shaw.
SERDP Project ER-1503, 94 pp, 2011

Comparison of stable isotope values between taxa within a particular site was used to link metal bioaccumulation in natural food webs to bioaccumulation and assimilation of metals by sentinel species. Results indicate that metal concentrations of Cd, Zn, As, Pb, and Se in sediments do not predict concentrations in biota, whereas sediment concentrations of Hg and MeHg do determine biotic exposures. Pelagic fauna bioaccumulate more MeHg than benthic feeding fauna, suggesting that chemical flux from contaminated sediments is important in determining bioaccumulation in pelagic food webs.

BSAF (Biota-Sediment Accumulation Factor)

A data set of approximately 20,000 biota-sediment accumulation factors (BSAFs) from 20 locations (mostly Superfund sites) for nonionic organic chemicals, e.g., PCBs, PCDDs, PCDFs, DDTs, PAHs, and pesticides. Fresh, tidal, and marine ecosystems are included in the data set, and species in the data set include fish and benthic species (e.g., lobster, crayfish, and benthic invertebrates). The purpose of the data set is fivefold: i) provides tools for evaluating the reasonableness of BSAFs from other locations, ii) provides a tool for building a BSAF data set for a specific location, iii) provides data for performing bounding assessments of risks for locations where limited or no bioaccumulation data are available, iv) permits inquiry into underlying relationships and dependences of BSAFs upon ecosystem conditions and parameters, and v) allows comparison of PCB, PCDD, and PCDF residues to residue-effects data download from PCBRes.


The potential for bioaccumulation, biomagnification, and toxicity vary within closely related groups of chemicals, such as PCBs and PCDDs/PCDFs. For example, the uptake, metabolism, elimination, and bioaccumulation of the PCB congeners differ among species. These differences can result in top-tier predators in a food web having different congener profiles to the sediment dwelling, benthic organisms at the base of the food web. This process is generally referred to as biotransformation, and may result in the concentration of a PCB congener in a species that is particularly sensitive to its toxic effects (USEPA 2005).

Adobe PDF LogoMemorandum: Response to Ecological Risk Assessment Forum Request for Information on the Benefits of PCB Congener Specific Analysis
Cleverly, D.
USEPA, Office Research and Development, NCEA-C-1315 ERASC-002F, 21 pp, 2005

TrophicTrace: Tool for Assessing Risks from the Trophic Transfer of Sediment-Associated Contaminants

Trophic Trace is an Excel-based spreadsheet tool that allows the user to calculate the potential ecological and human health risks (child and adult) associated with the bioaccumulation of contaminants in dredged sediments.