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  1. Home
  2. Choose Fish and Shellfish Wisely
  3. Building Fish and Shellfish Advisory Programs
  4. Designing a Fish and Shellfish Contaminant Monitoring Program

Multi-phase Approach Monitoring Strategy

The Multi-phase Approach Monitoring Strategy (Multi-phase Approach) consists of three phases – Phase 1: Screening Study, Phase 2: Verifying Magnitude of Contamination and Phase 3: Assessing Geographic Extent. When funding is limited, an Enhanced Phase 1 may be employed. The Enhanced Phase 1 involves more sampling than a typical Phase 1, but Phases 2 and 3 are not carried out.

On this page:
  • Objective of this approach
  • When should this approach be used?
  • Sampling Design Elements
  • Enhanced Phase 1 Approach

Objective of this approach

Phase 1 – Identify frequently fished sites, where commonly consumed fish and shellfish target species are found, to assess whether they are contaminated and may pose potential human health risk from consumption. This screening study entails sampling fish from multiple sites for chemical contamination where sport, subsistence, and/or commercial fishing is conducted.

Phase 2 – Assess and verify the magnitude of tissue contaminant concentration by resampling at sites that had fish tissue contamination in Phase 1.

Phase 3 – Assess geographic extent of contamination if necessary. In small to medium lakes, the fish contaminant concentrations may not vary spatially and may have been fully assessed in Phase 1 or 2. For larger lakes or lake systems, collect fish at additional sites. Another objective is to establish levels of relative contamination in 2-3 selected size/age classes of commonly consumed target species by analyzing tissue of fish with a range of lengths.

The allocation of limited funds to an Enhanced Phase 1 Screening Study or to the more intensive studies that include Phases 2 and 3 should always be guided by the goal of conducting adequate sampling of fish and shellfish resources to ensure the protection of public health. Sampling and analysis capabilities will be determined by available funding resources. Ideally, funding will be allocated for a Phase 1 Screening Study at as many sites as is deemed necessary while reserving adequate resources to conduct subsequent Phase 2 and 3 studies at sites where excessive fish tissue contamination is detected.

When should this approach be used?

The Multi-phase Approach is best when there are no fish contamination data from previous studies and funding is not the primary constraint.

Sampling Design Elements

Sampling Sites
Phase 1: Screening Study Phase 2: Verifying Magnitude of Contamination Phase 3: Assessing Geographic Extent
Sample target species where fishing occurs at sites that have an increased likelihood of contamination (based on observation or history) and at sites presumed to be uncontaminated. Sample target species at each site identified in the screening study where fish/shellfish tissue concentrations exceed human health fish tissue levels to assess the magnitude of contamination. Sample at additional sites in the waterbody to assess the geographic extent of the contamination in the waterbody.

Target Species and Size Classes
Phase 1: Screening Study Phase 2: Verifying Magnitude of Contamination Phase 3: Assessing Geographic Extent

Select target species from commonly consumed species using the following additional criteria - known to bioaccumulate high concentrations of contaminants and distributed over a wide geographic area.

Recommended: 

Inland freshwaters and Great Lakes – at least two fish species (including one bottom-feeder) and one mollusk if appropriate for the waterbody 

Marine/estuarine – at least two fish species (including one bottom feeder and one pelagic species), one mollusk, and one crustacean if appropriate for the waterbody

Resample target species at site where they were found to be contaminated in Phase 1. Target species found to be contaminated should be sampled at additional sites in the waterbody. Sample 2-3 size classes of the target species found to be contaminated in Phase 2.

Target Contaminants
Phase 1: Screening Study Phase 2: Verifying Magnitude of Contamination Phase 3: Assessing Geographic Extent
In many U.S. waters, fish are contaminated with multiple pollutants. Contaminants to Monitor in Fish and Shellfish Advisory Programs has the EPA's recommendations on contaminants that fish advisory programs should consider monitoring in fish and shellfish. Analyze only for those target contaminants from Phase 1 that exceeded human health fish tissue levels.

Sampling Times and Frequency

Sample during legal harvest season when target species are most available to consumers. Ideally, sampling time should not include the spawning period for target species unless the target species can be legally harvested during this period. Sampling frequency depends on program resources, but it is recommended that sampling be conducted at a frequency that is representative of the species class and size that consumers have access to over a typical fishing/shellfish harvesting season. Determine the need for additional sampling based on deficiencies in the samples collected to date.


Individual, Composite, and Other Sample Types Fish or Shellfish
Phase 1: Screening Study Phase 2: Verifying Magnitude of Contamination Phase 3: Assessing Geographic Extent
Collect sufficient fish for either individual or composite samples (5 individual fish processed together as a single sample). for each target species. Fish may be processed as fillet or whole as determined by the consumption habits of the target population. Collect, process, and analyze composite samples of edible portions of target shellfish species. Same (individual or composite) as Phase 1 screening study. Same as phase 1 screening study but collect composite samples for two or three size classes of each target species as appropriate.

Note: Program staff may opt for individual whole fish samples, or individual fish plug samples.  Although the skin-on fillet-based sample is the general recommendation for fish consumption advisory sampling, additional information can be obtained by analyzing other sample types. Sample type should reflect dietary and fish preparation methods of the target audience of concern.


Quality Assurance and Quality Control

Quality assurance (QA) and quality control (QC) measures ensure the precision and accuracy of the data collected. QA refers to the broader plan for ensuring quality in all aspects of a program and QC measures are the steps taken to determine the validity of specific sampling and analytical procedures. The Quality Assurance Project Plan describes in comprehensive detail the necessary QA/QC requirements and other technical activities that must be implemented to ensure that the results of the environmental information operations performed will satisfy the stated performance and acceptance criteria.


Sample Analysis

Use uniform analytical methods throughout the fish monitoring program for repeatability and comparability across the jurisdiction. Consider analytical method sensitivity and ensure that the sample processing lab is using appropriate method detection limits. Also consider method sensitivity when coordinating field logistics. Ideally, a jurisdiction would use only one laboratory per analyte class because inter-laboratory variability could complicate interpretation if multiple laboratories are used.

Enhanced Phase 1 Approach

An Enhanced Phase 1 involves more sampling than a typical Phase 1 and Phases 2 and 3 are not carried out. An Enhanced Phase 1 may be unavoidable if monitoring resources are limited or if an advisory must be issued based on detection of elevated concentrations in one composite sample. If monitoring resources are severely limited, precluding performance of any Phase 2 or 3 activities, EPA recommends three sampling options for collecting additional samples during the Enhanced Phase 1. These options are:

  1. Collect replicate composite samples for each target species.
    • This option provides additional information on size-specific levels of contamination that may allow fish monitoring programs to issue a fish consumption advisory for only the most contaminated size class while allowing the other size class of the target species to remain open to fishing. Assessors could analyze the composite sample from the largest size class first. If any human health fish tissue levels are exceeded, analysis of the smaller size class composite samples could then be conducted. This option, however, does not provide any additional information for estimating the variability of the contamination level in any specific size class. To obtain information for estimating the contamination level range in the target species, the protocol could be to separately analyze each individual fish specimen in any composite of a species that had been found to exceed the human health screening levels. However, this option of analyzing individual fish within a composite sample would increase analytical costs.
  2. Collecting replicate composite samples for each target species
    • This option provides additional statistical power that would allow the advisory team to estimate the variability of contamination levels within the one size class sampled. This option does not provide information on size-specific contamination levels.
  3. Collect replicate composite samples for each of two size/age classes of each target species found to be contaminated above human health fish tissue levels.
    • This option provides both additional information on size-specific contamination levels and additional statistical power to estimate the variability of the contaminant concentrations in both size classes of the target species. If resources are limited, you could analyze the replicate sample for the largest size class first; if the human health screening levels are exceeded, analysis of the smaller size class composite sample could then be conducted.

If the Enhanced Phase 1 results are the sole basis for developing a fish consumption advisory, this should be characterized as a more conservative fish consumption advisory.

Choose Fish and Shellfish Wisely

  • Should I Be Concerned about Eating Fish and Shellfish?
  • EPA-FDA Advice about Eating Fish and Shellfish
  • Eat Fish and Shellfish in a Healthy Way
  • How Do I Know if a Fish I Caught is Contaminated?
  • What the EPA Does to Protect You From Contaminated Fish and Shellfish
  • Technical Resources and Studies
  • Building Fish and Shellfish Advisory Programs
    • Designing a Fish and Shellfish Contaminant Monitoring Program
      • Integrated Approach Monitoring Strategy
      • Multi-phase Approach Monitoring Strategy
      • Sampling Sites
      • Target Species and Size Classes
      • Target Contaminants
      • Sampling Times and Frequency
      • Fish Sample Types
      • Shellfish Sample Types
      • Quality Assurance and Quality Control
      • Sample Analysis
    • In the Field - Collecting and Handling Samples
      • Sample Collection
      • Sample Handling
    • In the Lab - Processing and Analyzing Samples
      • Receiving Samples
      • Processing Samples
      • Analytical Methods
      • Quality Assurance and Quality Control
      • Data Verification, Reporting and Validation
    • Analyzing Data and Calculating the Consumption Limits
    • Developing a Fish and/or Shellfish Advisory
Contact Us about Fish and Shellfish Consumption
Contact Us to ask a question, provide feedback, or report a problem.
Last updated on December 23, 2024
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