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Project: EMAP Western Pilot

Background and Objectives

The Environmental Monitoring and Assessment Program (EMAP) Western Pilot was a seven-year effort led by EPA’s Office of Research and Development to create an integrated comprehensive coastal monitoring program to assess estuarine/marine condition along the West Coast (including California, Oregon, Washington, Alaska and Hawaii). The project objectives were to develop consistency in sampling design, sampling methods, data storage and data interpretation among the west coast states. The data collected as part of this program also represented the first consistent statewide data set for assessing consistency of estuarine benthic condition in California, and was instrumental for developing tools in support of California’s Sediment Quality Objectives.


This study was conducted from 1999 to 2006.


The program activities varied among years. The first year’s effort involved sampling the small estuarine systems in the States of California, Oregon and Washington. The second year focused on San Francisco Bay, the Columbia River and Puget Sound. The third year effort focused on Alaska and Hawaii. The fourth year focused on wetlands, with Southern California set aside as a special stratum that received more intensive effort. The fifth year focused on sampling of the west coast continental shelf. The last two years involved sampling in estuaries, similar to that in the first two years.

Year 1 (1999): The inaugural year of Western EMAP in California involved collection of samples at 80 sites in small estuaries. The program employed a stratified random sampling design, with the north coast estuaries treated as one stratum receiving 30 samples and the remainder of the State treated as a second stratum that received 50 samples. The indicators measured were the same as those measured by EMAP in other parts of the country, including:

Water Column

Dissolved Oxygen
Water Depth

Fish and Invertebrate Trawls

Species composition and abundance
Contaminants in fish tissue
Percent lipids


Grain size (% silt/clay)
Total organic carbon
Trace metals
Trace organics
Benthic species composition and abundance
Sediment toxicity

Year 2 (2000): Sampling in California in 2000 was limited to San Francisco Bay, which is the largest estuary in California. This estuary was not sampled in 1999 because it was of sufficient size to warrant its own stratum and there was insufficient funding to accomplish an additional stratum in the first year. The sampling design and indicators measured were identical to those in 1999, except that chemical measurements for dioxins and furans were added because of their particular concern in San Francisco Bay.

Year 3 (2001): No sampling was conducted in California in 2001. The primary activity in this year was to focus on enhancing consistency in data management among states. California also assisted EPA in training personnel from Alaska and Hawaii, which had more limited previous experience in regional monitoring.

Year 4 (2002): The 2002 program expanded on previous EMAP assessments of the subtidal habitat to sample the intertidal mudflat and emergent macrophyte (marsh) habitats. The sampling design consisted of 90 stations. Thirty of these were core sites at which the indicators measured were mostly similar to those measured by EMAP in the subtidal habitat. The differences were that fish were not collected and sediment toxicity was not measured. However, these were replaced by measures specific to this habitat (Table 1). Sixty additional sites, 30 in southern California and 30 in the San Francisco Bay region, were intensification sites at which additional intertidal indicators were measured. These additional indicators were measured only in California and served as a pilot effort for possible future EMAP expansion into the intertidal habitat.

Table 1. New core indicators measured in the 2002 intertidal sampling.

Year 5 (2003): The sampling program for 2003 consisted of 80 sample sites located in depths between 30 and 120 m offshore of the California coast. This was the first EMAP sampling to be conducted in offshore waters. The sampling design and indicators sampled were the same as in 1999, except that sediment toxicity was not included because of cost constraints. Sampling was broken into two zones. The first was the area north of Point Conception, where 46 sites were located. The remaining sites south of Point Conception were sampled as part of the larger Bight ’03 Regional Monitoring Program.

Years 6 and 7 (2004 and 2005): The last two years of Western EMAP in California involved collection of samples at 50 random small estuarine sites in each year. The indicators measured were the same as those sampled in 1999.


One of the goals of the wetlands effort was to establish a framework that could potentially be adopted by state agencies that are presently planning development of ongoing wetland monitoring programs. The effort was successful in that regard. Probabilistic designs and EMAP-type indicators that could be sampled on a single day have now become the core of California’s ongoing wetland monitoring efforts. In addition, coordinating the EMAP sampling efforts with the Bight Regional Monitoring program led to an even larger number of samples collected for EMAP purposes, as well as serving to further cement the cooperative relationship for future data collections in Southern California.


State Water Resources Control Board
San Francisco Estuary Institute (SFEI)
Moss Landing Marine Laboratories (MLML)
Oregon Department of Environmental Quality
Washington Department of Ecology


Data from 1999 EMAP

Data from 2000 EMAP
For more information on EMAP Western Pilot in California, contact Steve Weisberg at (714) 755-3203.
This page was last updated on: 7/1/2014