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Project: Assessing the Direct Effects of Sediment Contamination in the Sacramento and San Joaquin River Delta

Background and Objectives

Estuaries include bodies of waters at stream and river mouths that serve as mixing zones for fresh and ocean waters during a major portion of the year. Like marine bays, estuaries are a high priority for sediment quality assessment because they provide critical habitat for biological resources and receive contaminant inputs from many sources such as agriculture, urban runoff, and municipal wastewater. The goal of this project is to develop sediment quality assessment measurement tools and an assessment framework to evaluate the impact of sediment contaminants on benthic aquatic life within estuaries.

Like sediment quality assessment research in bays, estuary research included development of chemistry, toxicity, and benthic assemblage indicators, as well as the integration of these indicators for a multiple lines of evidence assessment. However, separate tools are needed for estuaries because different biological communities live in estuaries as compared to bays and different types or patterns of chemical contamination may be present. In addition, changes in salinity and other habitat factors may affect the chemical form of contaminants.

The objective of this project was to obtain synoptic data on sediment quality and biological resources in the Sacramento and San Joaquin River Delta for use in developing chemical indicators and benthic indices to support the State's Sediment Quality Objectives program.


This study was initiated in 2007 and completed in 2012.


Sediment quality surveys of the Delta were conducted in fall 2007 and spring 2008 in collaboration with the California Department of Water Resources, using a stratified random sampling design. A total of 144 stations were analyzed for acute toxicity to amphipods (Hyalella azteca); of these, a subset of 75 samples were selected for additional analyses of toxicity and sediment chemistry.


Toxicity of Delta sediments to H. azteca was low overall. Toxicity was detected only in the 2007 survey, with three percent of the stations causing a significant reduction in amphipod survival. A subset of 75 stations from both surveys were selected for the full suite of sediment quality triad analyses, including a second toxicity test (using Chironomus dilutus), benthic community analysis, and chemistry analysis.

Toxicity to amphipods was detected only in the fall 2007 Delta sediment survey.

The sediment chemistry results indicate contamination by legacy contaminants and current use pesticides is widespread in the lower Delta. DDTs, PAHs, diuron, and piperonyl butoxide were detected at more than 90% of stations. Pyrethroids (primarily bifenthrin and permethrin) were detected in about 30% of the samples. Analysis of the toxicity, chemistry, and benthic community data were used to develop sediment quality assessment tools for this region.


This project was conducted in collaboration with State Water Resources Control Board, San Francisco Estuary Institute, and California Department of Water Resources.

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