San Diego MS4 Permit Case Study

From Beachapedia

What is a Municipal Separate Storm Sewer System (MS4)?

An MS4 includes the conveyance or system of conveyances designed or used for collecting or conveying storm water that is not a combined sewer or part of a publicly owned treatment works. It includes roads with drainage systems, municipal streets, catch basins, curbs, gutters, ditches, man-made channels, or storm drains. These drainage systems typically dump their water (and any associated pollutants) directly into streams, bays, and/or the ocean.

What is a Municipal Separate Storm Sewer System (MS4) Permit?

The Regional Board issues an MS4 permit in order to establish the conditions under which pollutants can be discharged from the storm drain system to local streams, coastal lagoons, and the Ocean. The MS4 permit implements requirements of the Clean Water Act and Federal NPDES stormwater regulations. Since 1990, permits have been issued to municipalities based on their county location.

Federal regulations require that municipalities obtain this permit (known as a National Pollutant Discharge Elimination System, or NPDES, permit) and renew it every 5 years. Under this permit each municipality must develop a storm water management program designed to control the discharge of pollutants into and from the MS4 (or from being dumped directly into the MS4). The purpose is to protect local water bodies since storm drains typically dump their water into streams, bays, and/or the ocean without being treated. The State of California has the authority to issue this federal permit. Source:


After four previous MS4 stormwater permits, the San Diego region was still not been meeting water quality standards. To improve efficacy the Regional Board proposed a new regional permit and decided to shift the focus from a minimum level of actions to be implemented by the Copermittees (municipalities) to identifying outcomes to be achieved by those actions. However, Copermittees were concerned about increased cost from the new regulations and potential litigation if they were not immediately in compliance with the water quality standards, thus prompting their request for a “safe harbor” clause.

Situation Analysis

Polluted stormwater is the largest contributor to ocean pollution, and is the reason surfers are supposed to stay out of the water for 72 hours following a rain event in Southern California. The impacts of polluted urban runoff in Southern California are significant with 300 San Diego beach closures in 2011, and 750 beach closures in Orange County the same year. These impacts not only affect quality of life, but the tourism economy as well.

Due to a lack of specifications in previous MS4 permits, compliance had become essentially tracking numbers of actions and reporting, instead of tracking progress or actual improvements in the quality of receiving water or discharges from the MS4s.

To correct the situation the draft permit proposed to significantly modify the action-based approach of the current MS4 permits to an outcome-based approach, with a focus on achieving improvements in MS4 discharges and receiving water quality. A key feature of the draft permit was the inclusion of adaptive management, allowing Copermittees to select and address the highest priority water quality issues through an iterative process. This process is incorporated in watershed-specific Water Quality Improvement Plans (WQIPs), which are described in Provision B of the draft permit.

The WQIPs must be developed through a collaborative effort by the Copermittees in each watershed, key stakeholders, and representatives from the San Diego Water Board. The Water Quality Improvement Plans must include descriptions of the highest priority pollutants or conditions in a specific watershed, goals and strategies to address those pollutants or conditions, and time schedules associated with those goals and strategies. By allowing the Copermittees to expend their resources to address the highest priority issues, they will no longer be required to address “all pollutants, all of the time,” as was the premise of previous storm water permits. Thus making the draft permit a strategic, cost effective, and water quality outcome-based permit.


Although Copermittees have had more than 20 years to come into compliance with water quality standards, instead of acknowledging their limitations up to this point, they focused their efforts on attacking the cost and science associates with the draft permit; much like they have done with previous permits. The supposed increased cost to Copermittees was of great concern since it is estimated they already spend $120 million annually on stormwater in the San Diego region. Conversely, one could argue that the cost of non-compliance is of equal importance. Upon consideration of the cost of non-compliance in instances such as Aliso Creek, impacts to tourism from poor water quality, and health costs from illnesses, the cost to Copermittees seems more than justified.

The other major sticking point was the “safe harbor” clause, which Copermittees wanted as protection from enforcement actions since the new permit would hold them accountable for water quality standards. The “safe harbor” provision was essentially a “get out of jail free card” in that it would have allowed implementation of the Water Quality Improvement Plan to constitute compliance with Provision A.

Due to intense lobbying, the “safe harbor” clause was added to the draft permit at the eleventh hour, just two-weeks before the Regional Board hearing. However, after hearing from more than 25 activists at the April hearing, and receiving 200 letters supporting Surfrider’s comments the safe harbor clause was ultimately removed by the Regional Board at the May 8th, 2013 hearing.

Following a two-year stakeholder process the following concerns remained. Settling the concerns required policy decisions from the Regional Board.

  1. “Pre-development” vs. “Pre-project” as the baseline: Resolution the Regional Board kept the “pre-development” language and provided a better definition.
  2. Hydromodification exemptions were requested for concrete lined channels: Resolution the Regional Board added Hydromod exemptions for concrete lined channels.
  3. Weather or not to include TMDLs in the MS4 permit: Resolution the Regional Board decided TMDLS had to be included, and added some re-opener language. Furthermore, the Regional Board told Copermittees to pursue a Basin Plan Amendment if they felt the TMDLs were not “achievable”.
  4. Compliance with prohibitions and receiving water limitations: Resolution the safe harbor was added and later removed.
  5. What if 100% retention is not feasible on site? : Resolution If 100% retention is not feasible on site, the project must use biofiltraton for the stormwater volume x1.5 multiplier.


  1. Regional Water Quality Control Board (Region 9):
  2. Regional Water Quality Control Board (Region 9):
  3. Executive Officer Summary Report
  4. Revised Tentative Order No. R9-2013-0001 with Changes in Redline/Strikeout, released March 27, 2013
  5. TENTATIVE ORDER NO. R9-2013-0001Attachment F - Fact Sheet /Technical Report
  6. Regional Water Quality Control Board (Region 9): Final adopted permit

Appendices and Resources for Chapters:

  • Comment letter on administrative draft of MS4 permit Sept 14, 2012
  • Comment letter on the draft of the MS4 permit Jan 11, 2013
  • Summary of comments Jan 11, 2013
  • Surfrider San Diego’s stance on the revised draft permit
  • Appendix F, V: Regional MS4 permit approach
  • Activist Participation Guide for hearing
  • Sample Action Alert
  • Summary document re Copermittees perspective
  • PowerPoint with information from Copermittees
  • Language re retrofit of existing development in approved permit (pg. 105)

Questions for Discussion

  • Can this permit be used as a template for other parts of the County?
  • Moving forward, what are the best ways to increasingly incorporate LID for existing development into regulations?
  • How can Chapters partner with municipalities/copermittees to help them comply with permits like this and improve water quality?

News articles: Strict new stormwater runoff rules approved for San Diego KPBS San DiegoRegulators approve new standards on cleaning up stormwater Union-TribuneNew runoff pollution rules too costly? San Diego Union-Tribune

For information from the EPA about reducing stormwater costs through Low Impact Development (LID) click here.