San Diego Region SWAMP Monitoring, Assessment and Reporting

PHASE I - SWAMP Monitoring, Assessment, and Reporting (2000-2006)

From 2000-2005, the San Diego Water Board has been monitoring the Region’s 11 hydrologic units on a rotational basis. Water chemistry, water and sediment toxicity, benthic macroinvertebrate community, physical habitat, and on occasion tissue contamination, were assessed at multiple targeted sites twice during the dry and wet seasons. The monitoring was focused at the main stem of the rivers and streams, and major tributaries within the hydrologic units. In 2006, the data for the rotational watershed effort was summarized in watershed reports for each of the 11 hydrologic units. In addition, a synthesis report was produced for an evaluation of SWAMP in the San Diego region. The synthesis report and the watershed reports can be accessed at:

The synthesis report gives four main recommendations for SWAMP in the San Diego region: (1) Improve integrative and coordinated regional monitoring to increase cost-efficiency; (2) Design a probability-based study to address the ecological health of wadeable streams; (3) Use appropriate indicators, and (4) Build an information management system. Starting 2007, the San Diego region’s SWAMP implemented the recommendations of the synthesis report.

PHASE II - SWAMP Monitoring, Assessment, and Reporting (2007-2020)

Starting 2007, the four recommendations of the synthesis report were addressed and the new SWAMP monitoring design has included: (1) the coordination of regional monitoring (recommendation 1), (2) the planning and implementation of a probability-based stream monitoring program (recommendation 2), (3) the addition of indicators to the bioassessment program (recommendation 3), and (4) the development of statewide and regional data access portals (recommendation 4). In addition, SWAMP in the San Diego region added a section on special studies.

Coordination of Regional Monitoring:
SWAMP has initiated a project to improve monitoring and assessment of surface waters in the San Diego River watershed through collaboration and coordination with stakeholders. The goal of the project is to develop a coordinated and cost-effective monitoring and assessment plan for the San Diego River watershed. The project employs a multi-stakeholder, collaborative approach and is facilitated by the Southern California Coastal Water Research Project (SCCWRP), and Dr. Brock Bernstein. SWAMP has also started a project on the collaboration and coordination of monitoring and assessment in San Diego coastal wetlands. These projects will serve as a model for future projects to improve monitoring and assessment in other areas and other types of waters, as part of the larger effort of the San Diego Water Board to better assess the health of San Diego Region waters.

  • Workplan of the San Diego River Watershed Coordination project
  • Workplan of the San Diego Coastal Wetlands Coordination project

Probability-Based Stream Monitoring Program:
This program is facilitated by the Stormwater Monitoring Coalition (SMC), which is a coalition of stormwater management agencies and the San Diego, Santa Ana, and Los Angeles Water Boards from Ventura to San Diego. SMC designed a five-year program for comprehensive stream monitoring for southern California’s coastal stream and rivers that integrated many elements of individual stormwater monitoring programs, individual regional water board monitoring programs, and other existing water quality monitoring programs. The SMC study is based on a probabilistic design which will produce an unbiased assessment of the health of streams and rivers in southern California. Sampling for the SMC program started in 2009, and the following indicators were collected throughout southern California: (1) Bioassessment (benthic macroinvertebrates and algae); (2) Riparian wetlands; (3) Water chemistry; (4) Water toxicity, and (5) Physical habitat (including the California Rapid Assessment Methods (CRAM)).  Sampling for the program will continue for the next four years with new sites sampled every year.

For additional information on the SMC program:

Addition of Indicators:
In 2007 and 2008, SWAMP focused its efforts on bioassessment studies on reference sites and on impaired sites in the San Diego region. These bioassessment studies included the use of algae as a second bioindicator in bioassessment studies in addition to benthic macroinvertebrates (BMIs). Algal indicators are one of the most promising of the new indicators because they provide different and complementary information to BMI assemblages. As primary producers, algae directly respond to nutrients, one of the major stressors in California’s ecosystems. Also, algae assemblages can be used not only to assess overall impairment but also to diagnose certain stressors (e.g. nutrient, organic enrichment). In addition, algae assemblages usually respond faster to environmental stress than BMIs which makes algae good indicators for short‐term environmental stress while BMIs indicate environmental stress over a longer time‐period. For these reasons, SWAMP included algae as bioindicators since 2007.

  • Workplan for the 2007/08 bioassessment study
  • QAPP for the 2007/08 bioassessment study

Regional Data Portal:
Data from the San Diego region’s SWAMP are disseminated to the public by a regional data portal. Monitoring data from dischargers, nonprofit organization, and other agencies in the San Diego region will also be included into the data portal. Access the regional data portal at:

Special Studies:
SWAMP in the San Diego Region now includes a section on special studies. Several special studies have been conducted over the past several years as follows, some of which are ongoing:

  • Development of bioassessment tools for determining condition of nonperennial streams during the dry phase

In 2016, the San Diego Regional Water Board began funding a study to develop biological indicators of stream condition for use in the dry phase of intermittent rivers and ephemeral streams. Ephemeral streams are a large component of watersheds throughout the State, yet they are often excluded from monitoring or management programs because of a lack of tools to assess their condition. They provide important habitat for aquatic and terrestrial wildlife, process nutrients, transport sediment, and provide an array of other services. Maintaining the health of ephemeral streams can sustain beneficial uses in downstream rivers and estuaries.

With support from the San Diego Water Board, the Southern California Coastal Water Research Project (SCCWRP) and California State University at Monterey Bay, collaborated on the development of protocols to sample several indicators of condition of dry-phase intermittent rivers and ephemeral streams - specifically, terrestrial and riparian arthropods, and mosses. These indicators are being used to: 1) validate an existing, lower-cost rapid assessment method (CRAM) for episodic streams, and 2) develop a higher-resolution index of condition for use in this stream type during the dry phase. The project team has developed a draft sampling protocol (see link below) and continued collecting and analyzing samples during 2017 to expand the dataset. In 2018, a draft condition index was developed and is being refined in 2019. Plans for the next phase of the project are to validate the index and work on other initiatives geared toward facilitating eventual implementation of the index for a variety of assessment purposes.


  • Development of a Monitoring and Assessment Framework for Submerged Aquatic Vegetation (SAV)

In 2017, the San Diego Regional Water Board began funding SCCWRP to update a monitoring and assessment framework for submerged aquatic vegetation (SAV), including the development of sampling protocols for SAV that speak not only to assessment of condition, but also of the quality of functioning of SAV beds. These beds are primary producers that provide multi-level structural habitat within nearshore soft-bottomed areas. They serve as nursery areas, stabilize sediments, improve water quality, and export energy to other habitats and organisms (e.g. migratory birds). Despite the importance of SAV within the San Diego Region and coastal areas across the state, inconsistent methods are currently used to document their spatial and temporal existence, and limited biological metrics exist to assess their health and functioning, thus rendering the Water Board unable to address a core Beneficial Use question: Are Our Aquatic Ecosystems Healthy? SCCWRP has convened a Technical Advisory Committee consisting of regional experts from a variety of institutions to provide guidance and feedback on indicators and monitoring approaches. Testing of draft protocols began in 2019, and a final protocol is anticipated in 2020.


  • Occurrence and Extent of Pharmaceutical and Personal Care Products (PPCPs) in San Diego Water Resources

State, local health and regulatory agencies are aware of the presence of contaminants of emerging concern (CECs) in the environment, but they have not developed a comprehensive strategy to address monitoring and regulatory actions regarding CECs. This study addresses PPCPs in wastewater discharges and ambient receiving waters in the San Diego region. Results from this study will be used to fill key data gaps on PPCPs in the San Diego region and to inform future monitoring and regulatory actions.


  • Conditions of Depressional Freshwater Wetlands in Southern California

The San Diego, Santa Ana, and Los Angeles Water Boards have determined that evaluation of the extent and condition of depressional wetlands (such as freshwater marshes, and wet meadows) will be a priority for the next several years as a new element of the cooperative regional monitoring and assessment in southern California. These Water Boards and the Southern California Coastal Water Research Project (SCCWRP) designed a study on the systematic condition assessment of southern California depressional wetlands. Depressional wetlands comprise approximately 45% of the State’s 3.6 million acres of wetlands. This condition assessment will allow future management actions to be better targeted toward addressing deficiencies and in improving beneficial uses over the long-term.


  • Occurrence and Extent of Cyanobacteria in the San Diego Region

In the past, microcystin-producing cyanobacteria were confirmed in Lake San Marcos in the Carlsbad watershed, San Diego County. There is evidence that cyanobacteria and microcystin also occur in other lakes/reservoirs, streams, and wetlands in the San Diego region but no monitoring program exists for cyanobacteria and microcystin in the San Diego region. Funding from SWAMP facilitated some of the first screening studies of cyanobacteria and their toxins in freshwater resources in the San Diego region.

  • Poster presented at the Eighth Symposium on Harmful Algae in the US (11/18/2015)
  • Brief Presentation about the poster
  • Report on prevalence of cyanotoxins in southern California waterbodies based on screening assessments and regional monitoring programs
  • Report on the first-year (2016) findings from a study of cyanotoxins along the land-sea interface in California
  • Fact sheet on stream benthic cyanotoxins in San Diego and beyond
  • Fact sheet on cyanotoxins in lentic water bodies