Skip Navigation LinksResearch Areas > Contaminants > Direct Effects in Bays

Project: Sediment Quality Direct Effects on Benthic Infauna in Bays

Background and Objectives

Evaluation of sediment quality is an essential step in assessing pollution impacts on the coastal environment. Many contaminants bind to sediments and can accumulate to harmful concentrations in coastal habitats. Because a complex array of sediment processes influence the exposure of marine life to sediment contamination, a multifaceted approach is needed to assess contaminant impact on ecosystems and human and wildlife health. To support California's Sediment Quality Objectives program, researchers at SCCWRP developed tools and assessment frameworks to measure both the direct and indirect effects of sediment contamination. This work applies to estuaries and bays along the coast of California. The sediment quality assessment tools developed by SCCWRP provide environmental managers with a more consistent and reliable scientific foundation for sediment quality assessments within monitoring and regulatory programs.

Direct Effects - Risk to aquatic organisms caused by direct contact with contaminated sediments.

Indirect Effects - Risk to humans, wildlife, or aquatic organisms through consumption of food containing bioaccumulated contaminants.

Rapid Indicators
Rapid Indicators
Concentration of contamination in sediments affects not only benthic invertebrates, but animals higher up the food chain, such as marine mammals, birds, and humans.

The objective of this research area was to develop measurement tools and an assessment framework to evaluate the impacts of sediment contaminants on benthic aquatic life within bays. Bays are found where headlands or harbor works enclose an area of oceanic water within an indentation along the coast. Some examples of bays in California are Humboldt Bay, Bodega Harbor, San Francisco Bay, Morro Bay, Los Angeles Harbor, Newport Bay, Mission Bay, and San Diego Bay. Compared to offshore areas, bays are generally more contaminated and have more severely impacted sediment quality. Later studies focused on estuaries and indirect sediment contamination effects on wildlife and human health.


This project was initiated in 2005 and completed in 2008.


Tool development efforts refined and calibrated methods to evaluate the three major elements (lines of evidence) of sediment quality assessment: toxicity, chemical contamination, and benthic community assessment. A database of matched toxicity, chemistry, and benthic community analyses for sediment samples was created and used for tool development. Then, an integration procedure was used to consolidate data from each line of evidence and allow sediment samples to be classified into one of five categories:

• Unimpacted
• Likely Unimpacted
• Possibly Impacted
• Likely Impacted
• Clearly Impacted


This project resulted in the development and validation of an integrated collection of tools, thresholds, and a data interpretation framework for assessing sediment contamination impacts on benthic community condition. The framework provided an objective means for using a triad-based approach in large-scale sediment quality assessments. Based on this technical foundation, the State Water Board’s narrative sediment quality criteria and assessment framework became effective in 2009, following US Environmental Protection Agency approval.

Sediment Quality Assessment Overview


Sediment Quality Assessment Methods

Sediment Quality Assessment Findings



City of San Diego Marine Biology Laboratory
Los Angeles County Sanitation Districts
Moss Landing Marine Laboratory
National Oceanic and Atmospheric Association
San Francisco Estuary Institute
University of California Davis, Marine Pollution Studies Laboratory
University of Minnesota

Data and Tools

SQO Database  (sediment chemistry, toxicity, and benthic invertebrate measurements)
User Guide for SQO database
Complete list of SQO tools 

More Information on Project Components:

For more information on Direct Effects in Bays, contact Steve Bay at (714) 755-3204.
This page was last updated on: 7/1/2014