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 Permit Reissuance

The following video of a Bay Area Regional Collaborative Board meeting includes a presentation on the Municipal Regional Permit Reissuance (beginning at around 35 minutes). The presentation provides a status update from January 2021 and an overview of the focus on resilient green infrastructure. It is a resource on green infrastructure that the Regional Water Board staff believe to be informative, and the Board members may view it: Bay Area Regional Collaborative on 2021-01-15 10:00 AM.

For general inquiries, or to request copies of MRP Annual Reports, Green Infrastructure Plans, Water Quality Monitoring Reports, Direct Discharge Plans, or other submittals, please email our MRP inbox:

Or, contact MRP staff directly:

Zach Rokeach at or (510) 622-2364

Imtiaz-Ali Kalyan at or (510) 622-2499

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

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

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.

  (Page last updated 9/10/21)