Reducing Priority Pollutants

Reducing Marin’s Priority Pollutants To Improve Water Quality

When a specific creek or bay is impaired by a priority pollutant and doesn’t meet State Water Resources Control Board (SWRCB) and EPA water quality standards, that water body can be assigned additional requirements that need to be met to limit the amount of the pollutant. These requirements are called Total Maximum Daily Loads (TMDLs) and there are TMDLs for sediment, pathogens, pesticides, Mercury, and PCB’s in Marin.

The SWRCB can similarly add an amendment with new requirements directly to all municipal stormwater permits for a priority pollutant that impacts water quality statewide. They are currently in the process of doing this for trash.

Special protections are also assigned for coastal State designated Areas of Special Biological Significance (ASBS). The tidal shoreline off the Bolinas Mesa is home to the Duxbury Reef ASBS which is recognized for it’s particular biological communities, that because of their value and fragility, need special protections to preserve and maintain natural water quality conditions from all pollutants. Learn more about Duxbury Reef ASBS.

MCSTOPPP assists Marin’s 11 municipalities and the county in developing and implementing plans and programs to address all of these pollutant issues.

Erosion is caused by wind, rain, and wear detaching soil particles where they can then be transported as sediment. While erosion and sediment transport is a natural process that is a vital part of the natural stream process, excess erosion and sediment transport from human activities can not only be very damaging to our creeks and wildlife but also clog storm drains, cause localized flooding, and restrict creek channels.

Many pollutants such as heavy metals, pesticides, PAH’s, and detergents bind to soil particles so sediment coming from the urban environment also carries many additional pollutants into our creeks, bays, and ocean. These pollutants are toxic to aquatic life and can remain in our waterways for decades.

Sources of Erosion and Sediment

While there are many sources of erosion and sediment in the urban environment, listed below are main sources in Marin and ways to reduce and eliminate them.

  • Construction and landscaping
  • Increased development and impervious surfaces
  • Vegetation removal
  • Bank erosion and alterations
  • Fire roads, trails and other private dirt roads
  • Social trails
Construction and Landscaping

Grading, vegetation removal, stockpiles, trenching for utilities and irrigation systems, and vehicles and equipment tracking sediment out into the street are just some of the activities that these types of projects need to address. You can find preventative measures, referred to as Best Management Practices (BMPs), for these and many other construction and landscaping activities on our Resources for Projects During Construction page including helpful brochures such as Dirt Can Hurt, Keep it in Place!

Increased Development and Impervious Surfaces

As areas are developed the native soil and vegetation that used to infiltrate and take up most of the water during rain events is covered up by impervious surfaces such as roofs, driveways, sidewalks, and streets. Where natural ground cover may only have 10% runoff during the rainy season, areas with 10%-20% and 35%-50% impervious surface will have double and triple the amount of runoff respectively!

Increased runoff means increased peak flows in our creeks. This not only leads to more frequent and severe flooding events, but also causes excess scouring and downcutting of the creek bed and increased erosion and sloughing along the creek banks. Less water infiltrating down to the water table also causes decreased spring and summer flows in our creeks.

To mitigate these effects larger new and redevelopment projects are required to install permanent features such as bioswales, cisterns, bioretention facilities, and rain gardens that are designed to infiltrate and treat stormwater runoff after (post) construction and mimic preconstruction conditions. These practices are referred to as Low Impact Development (LID). To learn more about these requirements and how to implement Low Impact Development practices visit our Post Construction Requirements and Low Impact Development Resources page and check out helpful brochures such as Slow the Flow, Keep Rain Onsite! and Slow It. Spread It. Sink It.

Vegetation Removal

Vegetation plays many key roles in preventing rain and wind erosion.

  • Trees, shrubs, and other plants provide a canopy that protects the soil from rain drops striking the soil directly and dislodging particles.
  • Their root structure binds soils and holds them in place which is particularly important for stability on hillsides and along creek banks, and preventing dust from wind. Note – Native plants work the best because they have a much deeper root structure than most non-native plants, require less watering, and are self-sufficient after they become established (typically 2-3 years).
  • They slow the flow of runoff allowing sediment particles to settle out, increasing infiltration, and reducing concentrated flows that cause rilling and gullying.
  • They reduce the amount of runoff by uptaking water and releasing it through transpiration.
Bank Erosion and Alterations

A stable unaltered creek with native vegetation and a riparian corridor will often see minimal bank erosion in an average rain year. Bank erosion is often an indicator of upstream or downstream impacts and/or creekbank alterations. Factors can include:

  • Higher peak flows caused by increased development and impervious surfaces
  • Increased stream velocity caused by upstream armored banks, channelizing, and constrictions (walls, rip-rap, fill)
  • Increased depth and eddying caused by a downstream restriction
  • Removal of trees, shrubs, and other vegetation from the creekbank
  • Failing walls and other armoring

If you are a creekside homeowner and you’re experiencing creekbank erosion, it’s important to identify why the bank is eroding before developing a solution. Remember that any work done in the creek or on its banks will need permits! There are resources to help you get started on our Everything Creeks! page including helpful brochures such as Repairing Creekbank Erosion or check out the flyer for the Marin Project Coordination meetings.

Fire Roads, Trails, and Dirt Roads

Without proper maintenance fire roads, public trails and other public or private dirt roads can erode or even washout sending large volumes of sediment into our creeks.

Social Trails

Social trails are created by pedestrians, bicycles, and vehicles not staying on designated walkways, paths, trails, and roads. The continual wear on these cut-throughs tramples existing vegetation and compacts soils which greatly inhibits any new plant growth. These bare dirt trails also often go vertically up and down slope making them highly susceptible to erosion or are along roadways and streams so the sediment directly discharges to storm drains and creeks.

Resist the temptation and stay on designated walkways, paths, trails, and roads!

Lagunitas Creek Fine Sediment Total Maximum Daily Load (TMDL)

Lagunitas Creek, the largest watershed in Marin County, flows from its headwaters on Mount Tamalpais to its mouth in Tomales Bay. The watershed supports federally listed populations of coho salmon, steelhead, and California freshwater
shrimp. In 1990, based on evidence of widespread erosion and concern regarding adverse impacts to fish habitat, the State Water Board listed Lagunitas Creek as impaired by sedimentation under section 303(d) of the Clean Water Act.

The SF Regional Water Quality Control Board then developed a Total Daily Maximum Load (TMDL) allocation for sediment within the Lagunitas watershed. The TMDL contains specific actions for attaining water quality objectives and supporting identified beneficial uses for that waterbody. In June 2014, the San Francisco Regional Water Quality Control Board adopted a Basin Plan Amendment which officially established a TMDL for fine sediment in the Lagunitas Creek watershed. The Basin Plan Amendment also included an implementation plan to achieve the TMDL and related habitat enhancement goals.

Paved Roads Assessment

As part of the implementation plan a Paved Roads Assessment was completed to identify potential sediment discharge issues along county maintained paved public roads. The report was completed in 2017 and the County is using it as road map to identify and implement projects to repair and replace roadways, roadside ditches, and culvert crossings.

Available Data Sources

The following documents, reports and studies provide further detail on the regulatory background, sediment assessment and road infrastructure in the TMDL project area.

Regulatory Background
Road Maintenance Guidelines
Trash isn’t just a problem, it’s an ongoing social epidemic that is polluting our waterways. In an effort to combat this problem the EPA developed trash reduction requirements that would need to be implemented through municipal stormwater permits.

In California the Regional Water Quality Control Boards have been adding these requirements into regional stormwater permit renewals for large cities and urban areas (Los Angeles, San Diego, and the greater San Francisco Bay Area) over the last 10 years.

The State Water Board will now be adding these requirements into the statewide stormwater permit for all of the smaller municipalities (including here in Marin) when they reissue them in 2021.

In 2016 MCSTOPPP began working with our municipalities and developing regional partnerships to better prepare for this very large and expensive new program.

Clean Marin
Clean Marin Banner

To reach the goal of keeping Marin litter free we are implementing a plan that brings everyone to the table so together we can break the life cycle of trash.

Clean Marin is a growing coalition of 20 agencies, volunteer groups, and non-profit organizations!

Clean Marin Action Teams

Clean Marin has developed four Action Teams to address the wide spectrum of activities that can be done by volunteers to affect change.

  • Volunteer Programs – Developing tools and providing support to encourage Clean Groups and plan cleanups throughout Marin.
  • Clean Highways – Working through volunteer and multi-agency partnerships to develop real solutions to reduce the trash load on our highways.
  • Outreach, Education, and Marketing – Developing web based and social media content, outreach materials and campaigns, and school and business programs to engage the public, promote events, and expand anti-litter campaigns.
  • Source Control – Assisting and expanding recycling and zero waste programs, developing model local ordinances and product bans, and improving consumer awareness.
Clean Marin Programs

The goal is to collectively develop and improve tools and provide the necessary support so any group, business, or individual can participate in Clean Programs and make a difference in their community or neighborhood!

  • Adopt-A-Spot Program – Adopt a Spot today and play an active role in maintaining the beauty and cleanliness of your neighborhoods, parks, schools, creeks, shorelines and downtowns!
  • Clean Business Program – Take the Clean Business Pledge and take an active part in keeping your community clean! It’s a free program and a great way to promote your business!
Visit Clean Marin to learn more!
Trash Requirements

While the final new permit language is not expected to be out until late 2020 or early 2021, the preliminary requirements are as follows:

  • Capture all trash 5 millimeters (cigarette butt) and greater that enter enters a municipal storm drain system from all Priority Land Use Areas.
  • Priority Land Use Areas shall include commercial, industrial, high density residential and mixed use, and all transit stops.
  • To achieve this each permittee will need to install, operate, and maintain any combination of full trash capture systems, multi-benefit projects, other treatment controls, and/or institutional controls.
  • Each permittee will have 10 years to reach full compliance, with milestones such as demonstrating an average reduction of 10% per year.

MCSTOPPP will continue working with all of Marin’s permittees to update and prioritize measures in their Trash Reduction Implementation Plans based on the final permit language. To meet these requirements many types of treatment and institutional controls will be considered and evaluated to determine their effectiveness such as:

  • Enhanced street sweeping
  • Designated street sweeping days and times
  • Trash cleanups
  • Individual catch basin trash capture devices
  • Large area underground treatment devices
  • Volunteer cleanup events
  • Clean business programs
  • Anti-trash ad campaigns
  • Stormwater bioretention facilities
  • Green streets projects
Visual Trash Assessments

To evaluate the amount of trash that is accumulating on our streets and sidewalks, an On-land Visual Trash Assessment is conducted for each street segment in Priority Land Use areas.

MCSTOPPP conducted thousands of dry and wet weather assessments in 2017-2018 on behalf of all 11 municipalities and the unincorporated county to develop baseline trash generates in all of their Priority Land Use Areas.

Trash Implementation Plans

Each municipality will need to submit a final Trash Reduction Implementation Plan outlining how they will meet the requirements over the 10 year period ending December 31, 2030.

cartoon of pathogensAs well as being a countywide issue, Richardson Bay in East Marin and Tomales Bay in West Marin are both regulated under TMDLs for excessive levels of pathogens that cause water quality impairments.

Pathogens at elevated levels can pose health risks to humans and aquatic life alike.

Read more about what pathogens are, their potential sources, and what can be done to keep them out of our waterways, improve water quality, and keep our bays safe and clean.

What are Pathogens?

So what are pathogens? Simply put, they are parasitic organisms capable of causing disease in their hosts.

The waterborne pathogens that are causing the impairments in our bays are of fecal origin and made up of 3 groups of microorganisms:

  • Viruses – (Poliovirus, Hepatitis A)
  • Bacteria – (E.coli, Salmonella, Brucella)
  • Protozoa – (Cryptosporidium, Giardia)
Pathogen Sources

There are many potential sources of waterborne pathogens, but here in Marin they can generally be broken down into two categories.

Human Sources
  • Failing septic systems
  • Faulty or clogged sewer laterals
  • Boat discharges
  • Sewage treatment facility overflows
Animal Sources
  • Animal agriculture – dairies, grazing lands, horse facilities
  • Municipal runoff – pet waste
  • Wildlife
Pet Waste

Whether you gaze at Richardson Bay, play in the surf at Stinson Beach, hike to the heights of Mt. Tam, or stroll along Corte Madera Creek, the beauty of Marin will captivate you and keep you coming back for more. But when pet waste is improperly disposed, it can be picked up by water and washed into storm drains or directly into local creeks, bays or the ocean. Once in the water, pet waste contributes pathogens and nutrients that can negatively impact water quality. One of the ways that state and local agencies are working together to reduce the amount of pathogens found in our waterways is by eliminating the urban sources from the surrounding land.

Dog Waste

Did you know there are more than nineteen thousand licensed dogs with the Marin Humane Society? That’s more than fourteen thousand pounds of dog poop a day! To protect the water quality in our creeks, bays and ocean, and the health of our families it is important for all dog owners to pick up after their pets!

  • Always bag your dog’s waste and throw it away in the trash (NOT the green bin)
  • Pick it up and pack it out when enjoying one of Marin’s dog-friendly hikes or walks around your neighborhood
  • Pick up pet waste in your yard – pathogens will stay for months to years and put you, your family, and the environment at risk
  • Don’t use pet waste for fertilizer or bury it where food will be grown
Cat Litter

Dispose of kitty litter and cat waste properly by bagging the used litter and place it in the trash. Sanitary Districts do not allow flushing cat litter down the toilet. Even kitty litter made from pine or other natural materials cannot be placed in vegetable gardens or compost piles. If the cat waste carries pathogens, the temperatures in sewage treatment plants, composters, and digesters may not reach the high temperatures needed to kill the pathogens.

Rabbit, Tortoise and Small Animal Litter

Like kitty litter, soiled small animal litter and bedding material should be put in the garbage. The waste can also carry pathogens.

Horse Owners and Boarding Facilities
Stewardship on horse property is a major opportunity and responsibility. Topics on caring for the land, managing manure, and giving practical solutions to horse owners on what can be done to help protect the environment can be found on our main Horse Owners and Boarding page. Whether an owner has one horse or operates a boarding facility, all equestrians play an important role in assuring that our watersheds are healthy and our creeks clean.

OWOW store  displayPesticides are a statewide water quality issue. Where there is urban development and agriculture, there are pesticide toxicity issues in the waterways. That is why Marin County is under the same Urban Creek Diazinon & Pesticide Toxicity Total Maximum Daily Load (TMDL) as the entire San Francisco Bay Area.

MCSTOPPP works with programs such as Our Water Our World and the Marin County Pesticide Reduction Outreach Campaign to promote the use of less toxic pesticides and the overall reduction of pesticide use in Marin. In addition, each municipality and the County implement Integrated Pest Management (IPM) Programs to reduce pesticide use in their municipal operations.

MCSTOPPP also partnered with the City of Petaluma to develop and implement a regional pesticide monitoring program to determine if pesticides were present, and if so, which pesticides and at what levels.

If you have pesticides you no longer use, take them to your local household hazardous waste facility. In California it’s illegal to dispose of any amount of unused pesticide (or any hazardous waste) in the trash, in spite of what the label may say. You may dispose of empty pesticide containers in the trash if they are five gallons or less in capacity. When you have used up the pesticide, rinse the container three times, each time pouring the rinse water on the plant you bought the pesticide for. Then put the rinsed container in the trash. Water used to rinse out a sprayer or applicator should be applied like the pesticide.

Never dispose of pesticide rinse water in any indoor or outdoor drain or in the gutter!

Eco-Friendly Pest Control

MCSTOPPP is dedicated to practices that protect and enhance our creeks, bays and ocean. Such practices foster healthy soil, water conservation, runoff and waste reduction, and the use of the least toxic practices for managing pests.

To learn more about eco-friendly and effective ways to manage pests check out our Eco-Friendly Pest Control and Landscaping page.

Be a part of the Solution! Choose effective, less-toxic or non-toxic alternatives!

Education and Outreach Partners

To address pesticide-related toxicity in urban water bodies, MCSTOPPP partners with regional education and outreach programs in efforts to decrease demand for pesticides that threaten water quality, while increasing awareness of effective, less toxic alternatives.

Research done during development of the TMDL found that pesticides applied around homes according to label instructions can and do lead to toxicity in local water bodies. Education and outreach initiatives funded by State grants, wastewater and stormwater dischargers, and others like MCSTOPPP promote the behavior change necessary to reduce this threat of pesticide-related toxicity in our creeks. These initiatives include:

  • Our Water Our World provides materials, including fact sheets displayed at Bay Area hardware stores and a helpful free app, developed to assist consumers in managing home and garden pests in a way that helps protect water quality.
  • Department of Pesticide Regulation combines regulatory action and voluntary adoption of improved pest management methods. Their Pest Management Program encourages the use of environmentally sound pest management, including integrated pest management (IPM).
  • Yard Smart Marin started in 2016 as a county sponsored public-private coalition for pesticide outreach and education and became a fiscally sponsored project of MarinLink in 2019. The coalition includes individuals representing a wide range of organizations and perspectives from around Marin. They’re a quick one stop resource for safer alternatives to using pesticides. Whether it’s in the yard or inside your house, find solutions in just one or two clicks of the mouse!
  • EcoWise Certified is an independent, third-party certification program that distinguishes knowledgeable, leading-edge licensed pest management professionals who practice prevention-based pest control.
  •, hosted by Wastewater and Stormwater Dischargers, provides useful information on preventing all types of pollution where we live, work, and play, including how to find a certified pest control professional near you.
  • IPM seminars are offered in the Bay Area by the Pesticide Applicators Professional Association (PAPA), a non-profit corporation dedicated to providing Continuing Education and to the implementation of safe and effective pest control techniques. Look for “IPM” next to the seminar date.
  • Bay-Friendly Landscaping and Gardening is an approach to gardening and landscaping that works to maintain the natural conditions of the San Francisco Bay Watershed by fostering soil health, water conservation, waste reduction, and pollution prevention.

Rainfall and over- irrigation create runoff that can wash pesticides from landscaped areas and areas around buildings into storm drains and eventually into creeks, bays, and the ocean. In the 1990s, water from San Francisco Bay Area urban creeks proved toxic to aquatic organisms at the base of the food web, primarily due to runoff of the common insecticide diazinon. Diazinon was used throughout the Bay Area to manage many pests, including ants and grubs. The Diazinon and Pesticide-Related Toxicity in Urban Creeks TMDL plan (2007) sets forth actions designed to restore water quality.

By 2005, the Environmental Protection Agency required most products containing diazinon to be removed from retail store shelves. However, other pesticides with equal or greater aquatic toxicity have replaced diazinon and other banned chemicals in the marketplace. Therefore, the TMDL plan addresses pesticide-related aquatic toxicity in general, regardless of which pesticide causes the toxicity.

To comply with required TMDL actions, Marin’s cities, towns, and the County of Marin implement pesticide-related toxicity control programs. Each municipality adopted an Integrated Pest Management (IPM) policy or ordinance. IPM policies and ordinances require staff training and protocols and practices that result in less toxic pest management at municipally-owned and operated facilities.

As part of the education and outreach requirements, MCSTOPPP partners with other state and regional programs to promote pesticide reduction and the use less toxic alternatives.

Municipal Integrated Pest Management (IPM) Policies
Mercury sampling in Soulajule Reservoir

There are two separate Mercury TMDLs in Marin. The East Marin corridor is subject to the San Francisco Bay Mercury TMDL, and in West Marin the Walker Creek Mercury TMDL covers the Walker Creek and Soulajule Reservoir watersheds.

Mercury accumulates in aquatic species over time. Based on what they eat and how long they live, certain fish and shellfish species will accumulate higher concentrations than others and can reach unsafe levels for human consumption. See the tab below for safe seafood consumption guidelines.

Sources of Mercury
San Francisco Bay

The main source of most of the mercury pollution in San Francisco Bay dates back to the Gold Rush of the 1800’s, when mercury was mined throughout the Coastal Range and used in the Sierra Nevada to extract gold. All that mercury washed down the creeks and rivers and settled out in the bay. To this day, the single largest source is the Central Valley, where rivers continue to carry mercury from remote regions of California to the bay. Every time the mercury-laden sediment in the bay is disturbed, re-suspension of these historic deposits occurs.

Other sources for mercury in the San Francisco Bay include:

  • annual runoff from historic mines
  • municipal wastewater discharges
  • industrial wastewater discharges
  • urban runoff
  • atmospheric deposition

The sources of mercury entering the San Francisco Bay from along the East Marin corridor come primarily from the last four sources.

Walker Creek

The main sources of mercury in the Walker Creek and Soulajule Reservoir watersheds are mercury-laden sediment originating from inactive mercury mine sites. Since the entire watersheds consist of rural agricultural lands, there are not the same source issues from municipal or industrial discharges or urban runoff. While atmospheric deposition is ubiquitous across all landscapes, there is far less impervious surface that creates concentrate flows in these watersheds.

Mercury Pollution in Seafood
Exposure to mercury can cause a host of harmful health effects, including, birth defects, blindness, paralysis, and neurological and muscular disorders. Both naturally-occurring mercury and mercury pollution are found in sediment and water in creeks, rivers, bays, oceans and other water bodies. When mercury gets in our waterways, it can bio-accumulate in aquatic species and those that eat them.

Bioaccumulation is the process by which mercury builds up in organisms like plankton, small fish, large fish and people over time, since these organisms absorb mercury faster then they eliminate it.

Biomagnification is the process by which mercury becomes more concentrated as it passes up the food chain. This exposes those higher on the food chain, like large fish and people, to more mercury than those lower on the food chain, like plankton and small fish. Both of these processes result in mercury in your fish and on your plate.

So should I eat fish caught in San Francisco Bay?

Certain types of fish and seafood have been tested and found to contain high levels of mercury and polychlorinated biphenyls (PCBs) than others, and these harmful pollutants aren’t just in the San Francisco Bay and it’s source waterways. That’s why if you eat fish, be sure to choose the right type and amount of fish for your gender and age to avoid unsafe levels of mercury and PCBs. Follow the gender and age-specific guidelines in, “A guide to eating San Francisco Bay fish and shellfish” (PDF) issued by the California Office of Environmental Health Hazard Assessment (OEHHA) to limit consumption of these pollutants.

In addition to following the guidelines, make sure to trim off skin and fat, remove the guts, cook thoroughly, and drain juices. Fish skin, guts, livers and fat contain about half of the PCBs found in a whole fish. Mercury may also be present in fish livers and other organs. Remove these parts of the fish, cook the fillet thoroughly and drain the juices to reduce your exposure to these harmful chemicals.

Additional Resources

OEHHA factsheet on consuming fish from San Francisco Bay (PDF)
OEHHA San Francisco Bay Health Advisory FAQs (PDF)
Natural Resources Defense Council wallet guide to eating fish from any water body (PDF)
Seafood Watch west coast pocket guide to ocean-friendly seafood (PDF)

Reducing Mercury
below are main sources in Marin and ways to reduce and eliminate them.

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San Francisco Bay Mercury TMDL

On February 12, 2008, the U.S. Environmental Protection Agency approved a Basin Plan amendment incorporating a TMDL for mercury in San Francisco Bay and an implementation plan to achieve the TMDL.

Read more about the San Francisco Bay Mercury TMDL.

Walker Creek Mercury TMDL

On September 29, 2008, the U.S. Environmental Protection Agency approved the Basin Plan amendment incorporating a TMDL for mercury in the Walker Creek and Soulajule Reservoir watersheds.

The implementation measures for this TMDL are being conducted by the San Francisco Regional Water Quality Control Board and the Marin Municipal Water District. Read more about the Walker Creek Mercury TMDL.

Illustration of the many ways that trash gets into creeks

About PCB’s issues…

Sources of PCB's
Other PCB Info?

More info here…

PCB Implementation Plans

PCB’s reduction programs…