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Project: Assessment of Coastal Watersheds in the San Diego Region

Background and Objectives

Watershed managers require regional data to develop biomonitoring tools and contextualize local assessments. However, they often rely on data generated by programs with a more local emphasis, such as studies mandated by pollution discharge permits. These programs typically study only specific sites or stream reaches. The goal of this study was to compile individual data sets from site-specific programs to see if they could be merged into a regional-scale program. The compiled data was used to address three objectives:

1) Perform a regional assessment of stream health in Southern California;
2) Identify potential stressors to aquatic life in these streams; and
3) Determine how existing programs can be modified to better address the first two objectives.


This project was completed in 2008.


Water quality, toxicity, physical habitat, and benthic macroinvertebrate samples were collected from over 140 sites in coastal watersheds in San Diego, Riverside, and Orange Counties. Data were collected by six different programs including the State’s Surface Water Ambient Monitoring Program (SWAMP), California Department of Fish and Game, and multiple National Pollutant Discharge Elimination System (NPDES) monitoring programs. Watershed health was assessed by comparing each indicator to applicable thresholds. Scatterplots and multivariate ordinations were used to examine relationships among potential stressors and benthic macroinvertebrate communities.


The results indicated widespread impacts to many water chemistry constituents with some, like ammonia-N and specific conductivity, exceeding aquatic life thresholds in more than 60% of samples. More than 50% of water and sediment samples were toxic to at least one indicator species (Ceriodaphnia dubia, Hyallela azteca or Selenastrum capricornutum). Physical habitat was degraded (i.e., mean physical habitat score <10) at 30% of the assessed sites. Of the 708 bioassessment samples included in the study, 80% were in poor condition (i.e., index of biotic integrity <40). Impacts for all indicators were most severe in urban areas along the coast.

Graph of preliminary data from the statewide estuarine ambient assessment showing the distribution of estuarine acreage by habitat type.

Analysis for potential stressors indicated that multiple stressors likely affected aquatic life. Nonmetric multidimensional scaling of benthic macroinvertebrate communities identified two stressor gradients: a strong gradient associated with toxic contaminants in the water (e.g., metals and organics) and a weaker gradient related to nutrient enrichment (e.g., elevated nitrate and low dissolved oxygen). The toxic contaminant gradient was strongly associated with development in the watershed, and watersheds with more than 20% developed area were invariably in poor biological health.

Although data merged from multiple monitoring programs provided an assessment of stream health in the region, interpretations were limited due to a lack of coordination among programs. For example, the data set was undoubtedly biased because the individual programs typically focus on identifying impacted areas in order to address site-specific issues. As a result, the data set was not spatially representative, but instead focused on potentially disturbed areas to the exclusion of potentially healthy areas in the region.

Despite the potential for bias that limited the regional assessment, the merged data from multiple programs could be effective at evaluating stressors. The data captured important gradients in the region. However, diagnosing the specific causes of impairment at individual sites requires additional studies, where synoptic data are collected and analyzed.

Four improvements were recommended for the SWAMP program to enhance its ability to merge data from multiple programs. First, SWAMP should coordinate with other programs operating in the region in order to increase efficiency, share sampling sites, and save resources. Second, the monitoring program should utilize a probabilistic design where sites are selected randomly, rather than a targeted design, will eliminate bias and provide a more accurate picture of the overall condition of the region’s watersheds. Third, the monitoring program should identify a core set of indicators sampled synoptically at all sites to determine impacts to beneficial uses. These indicators should be selected in coordination with the other programs in the region. Many indicators examined in this report could work well, but others such as algae (to detect nutrient enrichment) should be considered. Fourth, ensure that there is an infrastructure to support collaborative programs. Consistent data structures, quality assurance requirements, and comparable field and lab methodology are essential for collaboration across multiple programs, and will greatly increase efficiency of bioassessments in the region.


San Diego Regional Water Quality Control Board


R Mazor. 2009. A multi-indicator assessment of stream health in southern California. Presented at 2nd Annual SCCWRP Symposium.
For more information on Assessment of Coastal Watersheds in the San Diego Region, contact Raphael Mazor at (714) 755-3235.
This page was last updated on: 7/1/2014