Monitoring and Assessment

The mission of the San Diego Water Board is to protect and restore the chemical, physical, and biological integrity of the waters in the San Diego Region. This mission is carried out through the implementation of the Board's authority to regulate discharges to the waters in the region. Assessing the progress or success of achieving the mission requires the collection of data and information through monitoring and reporting.

Historically, the Board primarily focused on monitoring the levels of pollutants in discharges to waters with limited monitoring of the quality of the waters receiving the discharges. This discharge-oriented monitoring approach can be used to assess compliance with regulatory requirements, but does not necessarily produce data or information that can be used to assess whether the conditions of the waters receiving the discharges are being protected or restored. Assessing the conditions of the waters receiving the discharges is needed by the Board to identify priorities, set goals, and realign work to focus the Board's limited resources on the key beneficial uses and key areas that are most important for the protection and restoration of the water quality in the San Diego region.

To that end, a water body-oriented regional monitoring framework was developed and endorsed by the Board in December 2012. The framework changes the focus of the Board's monitoring programs and requirements to the conditions of water bodies and collecting data and information on how to protect or restore the key beneficial uses of the water bodies in the San Diego Region.

As the framework is implemented and integrated into San Diego Water Board regulatory programs, the water quality monitoring data and information, and findings from assessments will be provided below.

Data and Information Resources

Assessments and Reports

Clean Water Act Section 303(d) and 305(b) Integrated Reports

Status Sheets

SWAMP Reports and Documents

Documents listed below are available upon request. Please contact Chad Loflen at

  • Molecular versus morphological approaches to generating algal taxonomic data for bioassessment applications (2020)
  • Methods and Guidance on Assessing the Ecological Functioning of Submerged Aquatic Vegetation in Southern California Estuaries and Embayments (2020)
  • Assessing the biological condition of dry ephemeral and intermittent streams (2019)
  • Coastal Habitats Trash Monitoring and Assessment Handbook (2019)
  • Field Protocol for Assessing Ecological Health of Dry-Phase Non-Perennial Rivers and Streams (2018)
  • Recommendations for a Southern California Regional Eelgrass Monitoring Program—2018 Update of Bernstein et al. 2011 (2018-July)
  • Development of a Monitoring and Assessment Framework for Submerged Aquatic Vegetation (SAV) (2018-June)
  • Fact Sheet of the San Diego SWAMP program (2018-January)
  • Assessment of episodic streams in the San Diego Region (2017-December)
  • Microcystin prevalence throughout lentic water bodies in coastal southern California (2017-September)
  • Assessing the biological condition of intermittent and ephemeral streams in the San Diego Region (2017- September) • San Diego Bay debris study (2016-October)
  • Benthic cyanotoxins widespread in California streams (2016-September)
  • Improving tools for monitoring multiple HAB toxins at the land-sea interface in coastal California (2016-July)
  • Development of molecular methods to identify stream algae (2016-June)
  • The prevalence of cyanotoxins in southern California waterbodies based on screening assessments and regional monitoring programs (2016-April)
  • Assessment of the condition of southern California depressional wetlands (2016-April)
  • Detection of caffeine in the streams and rivers within the San Diego region (2015-December)
  • Report on the detection of caffeine in the San Diego Region's streams and rivers
  • Historic Watershed Reports (2007)
    • San Juan Watershed Report
    • Santa Margarita Watershed Report
    • San Luis Rey Watershed Report
    • Carlsbad Watershed Report
    • San Dieguito Watershed Report
    • Los Penasquitos Watershed Report
    • San Diego Watershed Report
    • Pueblo San Diego Watershed Report
    • Sweetwater Watershed Report
    • Otay Watershed Report
    • Tijuana Watershed Report
    • Synthesis Report on Stream Assessments in the San Diego Region

Monitoring Programs

Regional Bioassessment Monitoring Program

The regional bioassessment monitoring program is a probability-based program and is facilitated through the Stormwater Monitoring Coalition (SMC). Documents listed below available upon request. Please contact Chad Loflen at

  • Documents (annual reports, special study reports, and fact sheets)
  • Ongoing Projects

Algae as Indicators for Water Body Conditions

The State of California is developing tools to assess water body health through algae as indicators. Documents listed below available upon request. Please contact Chad Loflen at

  • Molecular tool development for algae bioassessment
  • Algae IBI Abstract
  • Estuarine Eutrophication Assessment Abstract
  • California Streams Conditions based on Algae Indicators