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Stormwater runoff is generated from rain (and snowmelt) events that flow over land or impervious surfaces, such as paved streets, parking lots, and building rooftops. The runoff can pick up pollutants like trash, chemicals, oils, and dirt/sediment that can harm the San Francisco Bay and other surface waters including rivers, streams, lakes, and coastal waters. To protect these resources, communities, construction companies, industries, and others, use stormwater controls, known as best management practices (BMPs). BMPs prevent pollution by controlling it at its source and/or remove pollutants by treating stormwater prior to discharge.

The Water Board regulates stormwater discharges under authorities of the federal Clean Water Act and California’s Porter-Cologne Water Quality Control Act. We issue National Pollutant Discharge Elimination System (NPDES) permits for stormwater discharges from four sources: municipal separate storm sewer systems (MS4s), industrial activities, construction activities, and California Department of Transportation (Caltrans) properties and facilities.


Municipal Regional Stormwater NPDES Permit Reissuance

San Francisco Bay Regional Water Quality Control Board (Water Board) staff has prepared a Tentative Order for the National Pollutant Discharge Elimination System (NPDES) permit covering municipal stormwater discharges from entities in Alameda, Contra Costa, San Mateo, Santa Clara, and Solano counties listed in the documents linked below. The Tentative Order, also referred to as the Municipal Regional Stormwater Permit or MRP, will replace the Permittees’ existing permit.

Please see the Municipal Regional Permit Reissuance tab below for the Public Notice, the Tentative Order, and other information.

This tab contains information on the Municipal Regional Stormwater NPDES Permit and the Statewide Small MS4 Permit.

The Municipal Stormwater Program regulates stormwater discharges from municipal separate storm sewer systems (MS4s). An MS4 is a conveyance system designed to collect and convey stormwater that is owned by a city, town, or other public entity.

Urbanized areas increase stormwater runoff because impervious surfaces like roads, parking lots, and rooftops prevent stormwater from infiltrating, or soaking, into the ground. Urbanization also increases the variety and amount of pollutants in stormwater runoff. MS4s collect and convey this urban runoff and, in most cases, discharge directly to surface waters without treatment. Urban runoff contributes significant quantities of suspended solids, heavy metals, petroleum hydrocarbons, and other pollutants to surface waters of the region. However, if runoff is properly managed, those stormwater pollutants can be attenuated, and stormwater can be a valuable resource for uses such as groundwater recharge.

The Water Boards are actively involved in initiatives to improve the management of stormwater as a resource. Through permit requirements that promote low impact development (LID) techniques, green infrastructure (GI) planning, and other effective controls, we aim to prevent or minimize the discharge of pollutants contained in stormwater runoff to waters of the State.

Municipal Regional Permit

The Water Board issued county-wide municipal stormwater permits in the 1990s to all municipalities and flood management agencies in Alameda, Contra Costa, San Mateo, and Santa Clara counties, and within Solano County, the cities of Fairfield, Suisun City, and Vallejo, and the Vallejo Flood and Wastewater District. In 2009, the Water Board reissued these county-wide municipal stormwater permits as one Municipal Regional Stormwater NPDES Permit (MRP). The MRP was reissued in 2015 and is scheduled for reissuance in late 2021. The current permit and related reports are available here:

  • Municipal Regional Stormwater Permit, Order No. R2-2015-0049, as amended by Order No. R2-2019-0004

  • 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 Zachary.Rokeach@waterboards.ca.gov or (510) 622-2364
  • Imtiaz-Ali Kalyan at Imtiaz-ali.kalyan@waterboards.ca.gov or (510) 622-2499
  • MRP Permittee Stormwater Programs

    Alameda Countywide Clean Water Program - Association of 14 cities in Alameda County, together with Alameda County, the Alameda County Flood Control and Water Conservation District, and the Zone 7 Water Agency

    Contra Costa Clean Water Program - Association of 19 cities in Contra Costa County, together with Contra Costa County, and the Contra Costa Flood Control and Water Conservation District

    Fairfield-Suisun Urban Runoff Management Program

    Santa Clara Valley Urban Runoff Pollution Prevention Program - Association of 13 cities and towns in Santa Clara Valley, together with Santa Clara County and the Santa Clara Valley Water District

    San Mateo Countywide Water Pollution Prevention Program - Association of 20 cities and towns in San Mateo County, together with San Mateo County and the City/County Association of Governments

    Vallejo Flood and Wastewater District

    Statewide Small MS4 Permit

    On February 5, 2013, the State Water Resources Control Board adopted a General Permit for Discharge of Stormwater from Small MS4s (Phase II) that became effective on July 1, 2013. The following municipalities within Region 2 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

    For questions, contact Joseph Martinez at Joseph.Martinez@waterboards.ca.gov or (510) 622-2304.

    Small MS4 Permittee Stormwater Programs

    City & County of San Francisco

    Marin County Stormwater Pollution Prevention Program - 11 cities and towns in Marin County, together with Marin County

    Napa Countywide Stormwater Pollution Prevention Program - Five cities and towns in Napa County, together with Napa County

    Sonoma County Water Agency

    The Tentative Order, including Fact Sheet, is available and posted below for a 60-day public review and comment period. Written comments must be received no later than 5:00 p.m. on November 16, 2021, and can be submitted to the following email address: RB2-MRP@waterboards.ca.gov. They may also be sent to: Derek Beauduy, San Francisco Bay Regional Water Board, 1515 Clay St., Suite 1400, Oakland, CA 94612.

    The Water Board will hold a public workshop hearing on October 12 & 13, 2021, where it will consider and receive public comments on the Tentative Order. Please refer to the Public Notice document linked below for further information.

    The Water Board plans to consider adoption of the Tentative Order at a hearing in February 2022.

    If you have questions regarding this matter, please contact Derek Beauduy at (510) 622-2348 or via email to RB2-MRP@waterboards.ca.gov.

    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.

    The Statewide General Permit for Stormwater Discharges Associated with Industrial Activities (Industrial General Permit) regulates industrial stormwater discharges and authorized non-stormwater discharges from industrial facilities in California. The Industrial General Permit is called a general permit because many industrial facilities are covered by the same permit but comply with its requirements at their individual industrial facilities. The State Water Resources Control Board (State Water Board) and Regional Water Quality Control Boards (collectively, the Water Boards) implement and enforce the Industrial General Permit. Industrial facilities such as manufacturers, landfills, mines, hazardous waste facilities, transportation facilities, and recycling facilities are typically required to obtain Industrial General Permit coverage.

    Senate Bill 205 requires regulated industrial businesses to demonstrate compliance with the Industrial General Permit when applying for a business license. You can learn more about the requirements on the State Water Board’s website at https://www.waterboards.ca.gov/water_issues/programs/stormwater/sb_205_business_license_requirements.html.

    The Industrial General Permit requires facility owners or operators to develop and implement a Stormwater Pollution Prevention Plan and monitor their facility in accordance with the permit.

    The Industrial General Permit regulates about 2,000 industrial facilities in the San Francisco Bay Region. All permit applications and reports are submitted through the Stormwater Multiple Application and Report Tracking System (SMARTS) at https://smarts.waterboards.ca.gov/. For more information, visit the State Water Board Industrial Stormwater Program webpage at http://www.waterboards.ca.gov/water_issues/programs/stormwater/industrial.html.

    For questions, contact us by email to r2stormwater@waterboards.ca.gov or leave us a voice message at (510) 622-2402.

    Construction projects that disturb one or more acres of soil, or that disturb less than one acre but are part of a larger common plan of development, are required to obtain coverage for stormwater discharges under the Statewide General Permit for Discharges of Stormwater Associated with Construction Activity (Construction General Permit).

    Construction activity subject to this permit includes clearing, grading, demolition, and disturbances to the ground such as stockpiling or excavation but does not include regular maintenance activities performed to restore the original line, grade, or capacity of the facility.

    The Construction General Permit regulates construction stormwater based on project-specific overall risk to water quality. This permit requires temporary and post-construction best management practices and measures to prevent erosion and reduce sediment and pollutants in discharges from construction sites. Projects are required to implement a Stormwater Pollution Prevention Plan (SWPPP) developed by a certified Qualified SWPPP Developer (QSD) and requires. Many California Board of Professional Engineers, Land Surveyors and Geologists have self-certified. In addition, the California Stormwater Quality Association (CASQA) has a lookup tool to find licensed QSDs: CASQA QSD Lookup Tool.

    The Construction General Permit typically regulates over 1,400 construction projects in the San Francisco Bay Region, though this number varies throughout the year as construction projects are started and completed. All permit applications and reports are submitted through the Stormwater Multiple Application and Report Tracking System (SMARTS) at https://smarts.waterboards.ca.gov/. For more information, visit the State Water Board Construction Stormwater Program webpage at http://www.waterboards.ca.gov/water_issues/programs/stormwater/construction.html.

    Special Responsibilities Due to Mercury Mines

    At construction sites located in the vicinity or downstream of a historical mercury mine, soils may contain mercury, a neurotoxin that threatens humans and wildlife. Mercury must therefore be included in the assessment of potential pollutant sources and a discharger may need to employ more robust and redundant erosion and sediment controls than are normally used at similar construction sites. To assist you in identifying if your site may be located in the vicinity or downstream of a historical mercury mine, maps of historical mercury mines in the San Francisco Bay Region are available at the links below. The pink triangles on the maps indicate approximate locations of historical mercury mines and areas shaded in red indicate approximate runoff flow paths. These maps are listed by county:

    Regional Map

  • Marin (west)
  • Marin (east) and Sonoma
  • Napa (west)
  • Napa (east) and Solano
  • Santa Clara
  • San Mateo
  • Prior to issuance of the California Department of Transportation’s first statewide stormwater permit (Order No. 99-06-DWQ), the Regional Water Boards regulated stormwater discharges from Caltrans’ storm drain systems with individual permits. On July 15, 1999, the State Water Board adopted, and subsequently reissued, a statewide permit to consolidate stormwater permits previously adopted by the Regional Water Boards. This statewide permit regulates stormwater and non-stormwater discharges from Caltrans' properties and facilities, and discharges associated with the operation and maintenance of the State highway system. Caltrans' properties include all Right-of-Way owned by Caltrans. Caltrans' facilities include, but are not limited to, maintenance stations/yards, equipment storage areas, storage facilities, fleet vehicle parking and maintenance areas and warehouses with material storage areas.

    More information can be found on the State Board Caltrans MS4 Program webpage: https://www.waterboards.ca.gov/water_issues/programs/stormwater/caltrans.html

    For questions, please contact Caltrans liaison Qi Yan at Qi.Yan@waterboards.ca.gov or 510-622-2499.


    Municipal Stormwater Program

    Derek Beauduy
    Phone: (510) 622-2348

    Municipal Regional Permit Inquiries:

    Small & Non-Traditional MS4 Permit:
    Joseph Martinez,

    Industrial & Construction Stormwater Program
    Margaret (Maggie) Monahan
    Phone: (510) 622-2377

    Industrial & Construction General Permits Inquiries: R2stormwater@waterboards.ca.gov

    Qi Yan, Qi.Yan@waterboards.ca.gov

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