Municipal Stormwater Program

Phase I - Municipal Regional Stormwater Permit (MRP)

The federal Clean Water Act (CWA) was amended in 1987 to address urban stormwater runoff pollution of the nation’s waters. In 1990, US EPA promulgated rules establishing Phase 1 of the National Pollutant Discharge Elimination System (NPDES) stormwater program. The Phase 1 program for Municipal Separate Storm Sewer System (MS4s) requires operators that serve populations of 100,000 or greater to implement a stormwater management program as a means to control polluted discharges from these MS4s.

The Water Board issued county-wide municipal stormwater permits in the early 1990s to operators of MS4s serving populations over 100,000 (Phase 1). On November 19, 2015, the Water Board re-issued these county-wide municipal stormwater permits as one Municipal Regional Stormwater NPDES Permit to regulate stormwater discharges from municipalities and local agencies in Alameda, Contra Costa, San Mateo, and Santa Clara counties, and the cities of Fairfield, Suisun City, and Vallejo.

Municipal Regional Stormwater Permit Order No. R2-2015-0049

Documents associated with the development of the MRP can be obtained here:

Reporting on PCBs and Mercury Provisions

March 2017 final version of Interim Accounting Methodology (for loads avoided):

April 1, 2016 progress reports on identifying watershed management areas:

September 2016 reports on control measures to be implemented in the watershed management areas

Reasonable Assurance Analysis Workshop (September 23, 2015)

EPA Region IX and the San Francisco Water Board hosted a workshop on September 23 intended to inform Bay Area stormwater permittees on Reasonable Assurance Analysis (RAA).  RAA is a required component of the draft MRP 2.0 and linked to the requirement for all permittees to develop Green Infrastructure Plans.  However, RAA is a useful tool to support stormwater planning for both MS4 Phase I and Phase II permits. RAA uses analytical models to evaluate stormwater problems and verify a particular suite of management practices will be sufficient to ensure water quality goals are met. 

RAA efforts have already been performed in Cities of Los Angeles, San Diego, Paso Robles, and the Lake Tahoe Region, each of which were presented as case studies at the workshop.  In the Bay Area, the San Francisco Estuary Institute's Green Plan-IT tool is a likely option for performing the required RAAs under MRP 2.0, and was presented as a work in progress at the workshop. 

The workshop provided explanations about RAA by EPA and Water Board representatives. It also included presentations on each case study with a pair of speakers –the municipality or county  representative and the consultants who have developed the modeling tools in these different regions. Click on the links below to view the powerpoint presentations for the various modules or watch YouTube videos of the presentations to hear what the speakers presented.

Introduction: Dave Smith (EPA Region 9) and Tom Mumley (SF Bay Water Board) PDF watch video
Module 1: City Los Angeles (“Huub” Cox, City of LA and Steve Carter, Paradigm H2O) PDF watch video
Module 2: Paso Robles (Dave LaCaro, City of Paso Robles and Nicole Beck, 2NDNATURE) PDF (watch video)
Module 3: City of San Diego (Drew Kleis, City of San Diego) PDF (watch video)
Module 3b: LA Water Board (Renee Purdy) PDF  (watch video starts at 23:00)  
Module 4: Lake Tahoe (Peter Kraatz, Placer County and Chad Praul, Environ. Incentives) PDF (watch video)
Module 5: San Mateo County (Matt Fabry and Lester McKee, S.F. Estuary Institute) PDF

(watch video)

Synthesis and Next Steps: Keith Lichten (SF Bay Water Board) (no presentation available)    

Phase II

In 1999, the Phase II Rule automatically covered all small MS4s (not covered by the Phase I program) located in urbanized areas as defined by the Bureau of the Census. The State Water Resources Control Board issued a General Permit for Discharge of Storm Water from Small MS4s. The following municipalities are covered under this General Permit:

  • Marin County and its Cities
  • Napa County and its Cities
  • City and County of San Francisco
  • Solano County and the City of Benicia
  • Sonoma County and the Cities of Petaluma and Sonoma
  • Non-Traditional facilities that can include universities, prisons, hospitals, military bases, parks and office building complexes


Letter to local health departments and stormwater permittees outlining sidewalk sanitizing best management practices – October 2017

Staff Contacts:

Phase I Program:

Zach Rokeach: 510-622-2364;
(Alameda County, Santa Clara County, City of Fairfield, City of Suisun)

Zach Rokeach: 510-622-2364;
(San Mateo County, Contra Costa County)

Elyse Heilshorn: 510-622-2329;
(City of Vallejo, Vallejo Flood and Wastewater District)

Phase II Program:

Joseph Martinez: 510-622-2304;
(Marin County and its Cities, Napa County and its Cities, City and County of San Francisco, Solano County and City of Benicia, Non-Traditionals, Sonoma County and the Cities of Petaluma and Sonoma)