Engineering and Expeditionary Warfare Center

Sediment Sampling and Assessment

Sediment Sampling and Assessment


This section describes the types of characterization needed, methods used to collect samples and the assessments used to determine the risk posed by contaminated sediments at a particular site.  This information can then be used to make decisions on how best to manage and/or remediate the site.


Click on a Topic Below for more information

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Chemical Characterization


Chemical characterization includes measuring the concentrations of contaminants present in the sediment, and potentially other media including porewater, surface water, and suspended sediment, and determining the site geochemistry. Knowing contaminant concentrations at the site and throughout the contaminated watershed allows understanding of the source(s) of contamination, the fate of the contamination, and the level of risk to benthic and aquatic organisms and to humans.


Navy policy on the use of background chemical levels stresses that background chemicals must be eliminated from the list of chemicals of concern. The NAVFAC Guidance for Environmental Background Analysis: Volume II Sediment provides more information on determining background concentrations.


Navy policy also requires analytical laboratories to have specific certifications and follow rigorous quality assurance (QA)/quality control (QC) procedures. The Navy participates in the Department of Defense (DoD) Environmental Laboratory Accreditation Program (ELAP)


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Sediment Sampling Methods

Collecting specific sediment layers can provide information on the horizontal and vertical distribution of contaminants of concern throughout the sediment environment. A column of sediment, including the surficial (generally considered the top 5 to 10 centimeters or 6 inches) and underlying layers, can be used to document historical changes in the vertical distribution of contaminants of concern by characterizing the sediment quality with depth. Correlating potential organism exposure to specific sediment layers is important for determining any potential risk from exposure.

The physical characteristics of the area to be sampled are determining factors in selecting the proper sediment sampler. These physical characteristics include slope, bathymetry, flow velocity, sampling depth, and grain size as well as areal distribution of physically different sediment types to be sampled across an area. Surface grab samplers and core samplers are two methods used to collect sediment samples and are described below. Composite sampling is a useful design method to characterize a large area and is also described below.


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Surface Grab Sampling


Sediment grab samplers typically consist of a set of jaws that shut (clamshell) when lowered to the surface of the sediment. These samplers are easy to operate and can be used in a range of sediment types. The two most common grab samplers are the Ponar-style and the Van Veen style.


The Ponar-style grab sampler typically penetrates to 10 centimeters and can hold approximately 1 to 8.2 liters of sediment. The device can be used in both fresh and saltwater to collect samples of a variety of sediment types including hard sediments such as sand, gravel, consolidated material, or clay. The Van Veen grab sampler is designed for penetrating deeper into the substrate.


The Van Veen-style grab sampler can penetrate up to 30 centimeters and can collect between 8 and 75 liters of sediment. The device can be used in surging or rough seas without the risk of premature closure, where the grab closes as it is descending through the water column instead of when it hits the sediment surface, resulting in no recovery of sediment. The Van Veen grab is designed to descend vertically through strong underwater currents and collects samples without excessively disturbing the sediment.


Grab samplers are commonly used to collect sediment for the following reasons:

  • Larger volumes of sediment are needed for analysis
  • Consolidated, larger-grained sediments are expected to be encountered
  • Larger surface area of surficial sediment is needed
  • Surface water currents pose a sampling challenge


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Core Sampling


Core samplers are used to collect deeper samples or vertical profiles of sediment. The core sample can be used to characterize geologic conditions in the subsurface and document historical changes in the vertical distribution of contaminants of concern with depth.


Core samplers typically use weights, pistons, hydraulics, or pneumatic energy to drive a hollow tube into the sediment surface. The core samplers generally consist of a removable core liner, which fits into the core barrel and retains the sediment sample. Most core samplers can be used with different liner materials, including polyvinyl chloride (PVC), brass, thermoplastic polycarbonate, or stainless steel. These samplers can be used in a wide range of sediment types including fine- and medium-grained sediments, soft to semi-compacted material, and with plant roots in shallow bodies of water.


Two examples of core samplers are the piston core and the vibratory corer. The piston core can penetrate 3 to 20 meters and collect 5 to 40 liters of sediment. The piston core provides pressure for greater sample retention and can collect sediment samples in water up to 20 meters deep.


The vibratory corer applies vibratory energy and can penetrate 3 to 13 meters and collect 1.35 to 37.7 liters of sediment. The vibratory corer is designed to collect sediment samples from varying sediment environments (e.g., lakes, bays, and estuaries) and can be deployed in very deep water. It is typically constructed of stainless steel and can be powered by a portable generator.

Core samplers are commonly used when one of the following situations applies:

  • Characterization of deeper sediments is needed
  • Documentation of historical changes in vertical distribution of sediment characteristrics is needed
  • Reduced oxygen exposure is needed for sample analysis
  • Soft, fine-grained sediments are expected to be encountered in substrate


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Composite Sampling


Composite sampling consists of combining and thoroughly homogenizing spatially discrete individual samples, and treating the combined sample as a single sample for analysis. The discrete samples are collected from areas where contaminants are expected to be randomly distributed and variability is expected to be low. Areas with elevated contaminant concentrations generally must be sampled separately with a discrete sampling design.

A benefit of composite sampling is that it can improve the spatial or temporal coverage of an area without increasing sample number. Composite sampling can also increase the ability to detect hot spots by increasing the number of locations sampled. A series of composite samples over a small area will result in a better defined exposure point concentration to be utilized in a risk assessment.


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Physical Characterization

Characterization of the physical environment is a key factor in understanding the possible depth and breadth of the sediment contamination at a location. Characteristics such as sediment grain size, sediment layer composition (e.g., changes in clay content), porewater seepage, gas ebullition, direction and velocity of groundwater or stream/river flow, wave or tidal actions, elevation changes/bathymetry, previous disturbances, and more can all play a role in the occurrence and distribution of contamination.

There are a variety of tools for conducting a physical evaluation of a sediment site.

  • Geophysical measurements include the use of acoustics or sonar to evaluate the sediment bed (e.g., bathymetry, side-scan sonar, and subbottom profiling).
  • Flux measurements include the use of piezometers, seepage meters, and gas-flux chambers.
  • Visual measurements include sediment profile imaging (SPI).
  • Biological/ecological measurements include organism/population surveys, habitat surveys, and wetland delineation.
  • Water quality measurements include turbidity, total suspended solids, pH, dissolved oxygen, and conductivity, as well as chemical analyses.
  • Geotechnical measurements include sedimentation rates, particle size distribution, and geological consistency and integrity (e.g., Sedflume erosion measurements).
  • Hydrodynamic measurements include sediment transport modeling and erosion modeling.



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Hydrodynamic Modeling

The use of hydrodynamic models helps to understand the shear forces that occur at the sediment water interface and subsequently how sediment transport can affect the fate of contaminants in the sediment system. Hydrodynamic models usually include the use of sediment bed models, contaminant transport models and, at times, food web models. Hydrodynamic models now provide formulas that allow computation of flows and sediment fluxes in two and three dimensions.

 Some common hydrodynamic models used include:

  • SEDZL: An EPA three-dimensional (3-D) model that predicts the settling, re-suspension, and deposition of coarse-, medium-, and fine-grained sediments
  • SMS-RMA2: A United States Army Corp of Engineers (USACE) two-dimensional (2-D) model that computes water levels and horizontal water velocities
  • EFDC: An EPA 3-D model that simulates complex water bodies such as estuaries, lakes, and coastal waters
  • CH3D: An USACE 3-D model that predicts water surface elevation and water velocity, and can model sedimentation


Hydrodynamic models tend to be complex models that require specific technical expertise to establish appropriate input and boundary conditions.


To perform sediment transport modeling, a comprehensive set of hydrologic, hydraulic, and sediment data must be collected/measured in the sediment system to be modeled.

Sediment transport modeling includes a variety of factors such as determining the depositional or erosional nature of an area, settling velocity, critical shear stress, bed density, bed shear strength, tidal flow conditions, and potentially other variables. Sediment transport is impacted by processes such as scour, deposition, erosion, resuspension, and bed shear. Each model requires different input variables. The results of sediment transport modeling can be used for a variety of needs such as determining sediment grain size and placement requirements for in-water capping projects or for determining sediment total maximum daily load (TMDL) requirements or whether exceedances of TMDLs have occurred.


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Ecological Characterization

Sediments are habitat for a variety of benthic organisms and several methods can be used to evaluate and analyze the benthic environment.


One method is to take an undisturbed, vertical cross-section photograph of the top 15 to 20 centimeters of the seafloor using an SPI camera. The SPI camera records digital images of the sediment-water interface and the sediment profile along the depth of penetration; then an analyst can evaluate the images for the following parameters:

  • prism penetration to estimate sediment compaction
  • surface relief to determine habitat characteristics
  • apparent color redox potential discontinuity (RPD) layer which is an important estimator of benthic habitat quality
  • sediment grain size
  • surface features (i.e., worm tubes, epibenthic organisms, algal mats, shells)
  • subsurface features (i.e., burrows, water filled voids, infaunal organisms)
  • faunal successional stage to determine whether the infauna are in pioneering or colonizing stages


Another method to evaluate the benthic community in sediment samples is to collect sediment grab samples and then sieve the sediment material through a mesh sieve or a series of mesh sieves. The material remaining after sieving is collected into jars and fixed (e.g., in 10% formalin). A qualified analyst at a benthic laboratory receives the samples, washes the samples to remove the formalin, and preserves the samples (e.g., in isopropyl alcohol or methanol). The samples are then sorted, identified, and counted to determine numbers of benthic infauna and the species present in each sediment sample. In addition, various statistical tests can be performed to assess species and population metrics, including relative abundance, and correlations can be made between site physical characteristics and ecological findings.


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Nature and Extent of Contamination

Characterizing the nature and extent of contamination is necessary to make informed decisions regarding the level of risk presented by a contaminated sediment site and the appropriate type(s) of remedial response. This process involves using the information from sediment characterization and physical site data to identify locations where contaminants are present and to understand the relative occurrence and distribution of various contaminant classes or individual contaminants.


A sampling and analysis approach should contain data quality objectives (DQOs) that consist of either (1) initially collecting a large number of samples for screening and then, based on the results of the screening samples, collecting additional samples for a more rigorous analysis, or (2) collecting all of the samples in one sampling event. Documenting the nature and extent of contamination using appropriate analytical methods and sensitivities to yield data that meet the DQOs are important for determining risk and selecting appropriate remedial alternatives. The results of various chemical and physical characterization methods that are employed, as discussed above, are all considered during the evaluation of the nature and extent of contamination.



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Contaminant Fate and Transport

The fate and transport of contaminants in sediment is largely dependent on sediment transport processes, as sediments are typically fine-grained and organic, which leads to strong adsorption of contaminants to the sediment matrix. Therefore, it is important to understand the sediment transport processes to be able to evaluate the fate of contaminants in the sediment system.

Some of the contaminant fate and transport models used are:

  • HEC-6R: A one-dimensional (1-D) sediment and contaminant fate model designed by USACE. This model integrates the hydrodynamics of water flow and movement of sediments into a simple system focusing on scour and deposition. When tracking contaminant fate, the model includes contaminant influx, sorption/desorption, radioactive decay, and bed-sediment layering.


  • EFDC: A 3-D EPA model that simulates transport in complex water bodies such as lakes, estuaries, and coastal areas. A unique quality of EFDC is that it can solve an equation describing the transport of suspended sediment, toxic contaminants, and water quality state variables.


Contaminant transport models are often integrated with hydrodynamic models and may require site-specific information.


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Toxicity and Bioaccumulation Testing

Risks to ecological receptors from direct exposure to contaminated sediment (and other related media such as porewater or surface water) can be assessed through laboratory or in-field toxicity studies. Risks to ecological receptors that accumulate contaminants in their tissues can be assessed based on bioaccumulation studies. Risks to ecological receptors can also be evaluated by comparing tissue concentrations with concentrations known to cause adverse effects. Click here for more information on the Navy's approach to ecological risk assessment (ERA).

Toxicity testing involves exposing an ecological receptor, typically a representative species, to the environmental medium of interest, and then observing the receptor over some duration of time for evidence of acute or chronic toxicological effects (e.g., reductions in growth or survival) relative to controls and reference thresholds for the observed effects. Common representative organisms include benthic invertebrates, bivalves, and fish.

Bioaccumulation models project how a contaminant would accumulate in the food web after a receptor is exposed to the contaminant. However, bioaccumulation models may not be necessary if tissue data are available. To simulate bioaccumulation, the rate of change of the contaminant concentration within the organism is taken into account. The factors that control the flux of the contaminant into and out of the organism include direct uptake of the contaminant from the sediment system, ingestion of the contaminant through feeding, and loss of the chemical by elimination and dilution of the chemical due to growth of the organism. A mass balance can be calculated for every trophic level to predict the concentration of the contaminant at any level.

Some of the toxicity and bioaccumulation models available are:

  • Biota Sediment Accumulation Factor (BSAF) Model: Developed by the EPA, it predicts bioaccumulation of hydrophobic organic contaminants in aquatic organisms based on sediment concentrations and partitioning coefficients.


  • Bioaccumulation and Aquatic System Simulator (BASS): Released by EPA, it is used to predict bioaccumulation within a fish community focusing on specific species of fish. BASS can model the accumulation of both metals (cadmium, copper, lead, mercury, nickel, silver, and zinc) and organic contaminants in fish.


  • Biodynamic Model of Bioaccumulation (DYMBAM): Developed by the United States Geological Society (USGS), it is used to predict the bioaccumulation of metal contaminants in organisms such as clams and ducks. DYMBAM uses a kinetic approach, which takes into account reaction rates and makes the model more flexible to changing conditions.


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Ecological Risk Assessment

Aquatic organisms, such as fish and invertebrates, and wildlife that use aquatic habitats may be exposed to contaminants in sediment through the following pathways:

  • ingestion (more often)
  • absorption (more often)
  • respiration of contaminant vapors (less often or limited)


To assess risks to ecological receptors, it is important to assess both direct and indirect exposure pathways:

  • Direct exposures result from direct contact with surface sediments, porewater, and/or the overlying water column, such as those which may occur for fish and invertebrates
  • Indirect exposures result from consumption of contaminated prey


Aquatic plants and benthic invertebrates serve as food for small fish, which are subsequently eaten by larger fish. These may then be consumed by wildlife that feed in aquatic habitats, such as birds and mammals. Some contaminants may bioaccumulate in organisms at concentrations that are greater than those present in the environment in a process called biomagnification.


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Human Health Risk Assessment

While direct contact through dermal exposure could be considered a complete pathway for human exposure to contaminated sediments, for most sites the primary exposure route is through consumption of fish that have accumulated contaminants from the sediment in their tissues. The assumption cannot be made that if surface water concentrations are below analytical detection limits, there is no risk to receptors.

As consumers continue to feed on contaminated prey, certain contaminants may accumulate in their tissues. The more hydrophobic (water-hating) a contaminant is, the higher the likelihood that it will remain in the tissues of an organism. Many hydrophobic contaminants are considered to be persistent, bioaccumulative, and toxic (PBT).

Risks to humans from indirect exposure to contaminants by consuming contaminated food are assessed in general by estimating daily dietary doses and comparing them with daily doses known to cause adverse effects. Risks from consuming contaminated food increase as the dietary dose increases (i.e., as the exposure increases). Therefore, receptors who consume contaminated items more often and in greater portions (e.g., subsistence fisherman) will have higher risks than a receptor who consumes contaminated items less often and in smaller portions (e.g., recreational fisherman).


Click here for more information on the Navy's approach to human health risk assessment (HHRA).


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Risk Management

Estimated risks are generally the basis for decisions about how to manage contaminated sediments. Depending on the magnitude of the risk, several options will be evaluated during the RI/FS phase ranging from active remediation (removal or treatment) to allowing the system to recover naturally.

It is important that risk estimates are made with the highest level of confidence possible to ensure protection of human and ecological health and to facilitate appropriate remedial decision-making. An example of a risk management framework is where the Navy's ERA approach is integrated with remedial decision-making. This will help to ensure that any remedial alternatives effectively reduce the risk to acceptable levels and consider residual risk and the ecological impact of implementing the remedy.

Risk management decisions can and should be made throughout the RI/FS process and should result in the selection of a remedy that is designed to reduce both human and ecological risks. Once the risk management decisions are made, they should be discussed and agreed upon with the appropriate stakeholders prior to proceeding with the evaluation of remedial alternatives.


General risk management principles include the following:

  • Controlling sources early
  • Developing a conceptual site model (CSM) that communicates information about site characteristics
  • Involving the community and coordinating with state and local governments
  • Selecting site-, project-, and sediment-specific risk management approaches to achieve appropriate remedial action objectives.
  • Ensuring that sediment cleanup levels are tied to risk management goals, and are site specific to the degree possible, attainable, measurable, and relevant
  • Designing remedies to minimize short-term risks while achieving long-term protection and being appropriately sustainable
  • Monitoring during and after sediment remedy implementation


Additional information on methods for remediation of contaminated sediments can be found on our Sediment Remediation Webpage







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