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Project Component: Development of Benthic Indicators

Background and Objectives

Because invertebrates that live in or on sediments are exposed to environmental stressors on an ongoing basis, the benthic life present at a particular location often provides a good indicator of sediment quality. Interpreting benthic community composition is challenging because the community can be impacted by other factors besides contamination, such as natural variations in habitat and physical disturbance. Benthic indices apply standard mathematical formulas to data on the number and diversity of benthic organisms at a particular location to find a score that rates the disturbance of the community. This provides a simple means for communicating complex ecological data to environmental managers. The objectives of this project were to evaluate the accuracy of benthic indices for describing the condition of benthic communities in California bays and to calibrate a suite of indices for use in California.

Benthic macrofauna communities in sediment are primarily composed of three types of organisms: molluscs (left), polychaete worms (center), and crustaceans (right).


This study was completed in 2008.


A comprehensive database containing regional monitoring results for California, Oregon, and Washington embayments was assembled and standardized. Cluster analysis of the data was used to determine the principal types of benthic assemblages along the West Coast. Five benthic indices were calibrated for two of the most prevalent habitat types in California and evaluated with respect to their accuracy in predicting benthic community condition for a sample data set. The basis for evaluating benthic index accuracy was the consensus evaluation of nine benthic ecologists who each evaluated the same data using their best professional judgment.


Benthic communities in California embayments were grouped into six major assemblage types that were associated with distinct habitat types differing in salinity, sediment particle size, and location. Evaluation of the indices showed that none of them were individually able to predict benthic community condition at a level of accuracy equivalent to expert judgment. Use of the indices in combination provided markedly better accuracy. A combination of four indices was recommended for used in sediment quality assessment: the Benthic Response Index (BRI), Relative Benthic Index (RBI), Index of Biotic Integrity (IBI), and River Invertebrate Prediction and Classification System (RIVPACS).


San Francisco Estuary Institute
Los Angeles County Sanitation Districts
City of San Diego Marine Biology Laboratory
Moss Landing Marine Laboratory
University of Minnesota


Direct Effects Assessment Sample Calculation  - Document describing the calculations needed to interpret chemistry, toxicity, and benthic infauna data for sediment quality assessment. Calculations are illustrated using a sample data set. 

Benthic Index Calculation Methods for California Embayments -  A description of the steps and calculations needed to apply four benthic indices. The steps include collecting data, calculating scores for each benthic index, comparing the benthic index scores to threshold values, and integrating the individual index results to determine the benthic community condition classification.

Species List of Embayment Macrofauna - List of benthic macroinvertebrate species found in California embayments, including their taxonomy, pollution tolerance scores, and notes for use in benthic index calculations.

Data and program files for calculating RIVPACS index scores using SAS - Program, habitat characteristics, and sample data files needed for calculation of the RIVPACS benthic index. User must have SAS software to run the program. Instructions for use are provided in "Benthic Index Calculation Methods for California Embayments."

Data files for calculating RIVPACS index scores using the Utah State University website - Habitat characteristics and sample data files needed for calculation of the RIVPACS benthic index using a web site. Website user ID and password are required. Instructions for use are provided in "Benthic Index Calculation Methods for California Embayments."

For more information on Development of Benthic Indicators, contact Steve Bay at (714) 755-3204.
This page was last updated on: 6/24/2014