Our Aquatic Gem
San Mateo’s best-known secret is its tranquil, inviting Marina Lagoon (Lagoon). Enjoyed by our residents, watercraft users, beach enthusiasts, and families of bird species from pelicans to sandpipers, our Lagoon is an amenity for all.
History – A Tidal Slough
A remnant of a tidal slough that was diked and dredged, our Lagoon now helps to protect our city from flooding, while offering a recreation area, wildlife, and ecological resource. Our staff manage the Lagoon optimize these benefits for all citizens.
Inlet: O’Neill Slough
Outlet: Seal Slough
Distance: 4.5 miles
Depth: Average 3 feet
Watershed: 10.3 mi2
Flow: North, controlled
Water Flow & Levels
The Lagoon’s primary water source is tidal flow from San Francisco Bay through O’Neill Slough during high tides. Bay water is augmented by perennial low volume freshwater inflow from Laurel Creek, Borel Creek, and other lesser drainages within a 10.3 square mile watershed. During the wet season, stormwater runoff can comprise a larger proportion of inflow over the short-term, depending upon the size of the storm event.
Find more details on our water levels webpage.
Water Quality in the Marina Lagoon
Water quality is an important factor contributing to life on the Lagoon. The Lagoon receives stormwater runoff from a majority of the City, and pollutants are carried through streets and storm drains directly to it. These pollutants include pesticides applied to residential and commercial landscapes, oil and grease from cars, litter, legacy pollutants such as mercury, and bacteria from animals, sanitary sewer overflows, and leaks.
We are subject to several regulatory requirements that direct us to perform certain activities and develop plans to limit and address these pollutants.
It is important to maintain healthy conditions for people who use the Lagoon area for recreational purposes, and for wildlife and fauna who make it their home.
San Mateo storm drains flow directly to the Lagoon without water treatment. We take every opportunity to remind our residents to report stormwater pollution.
Help us spread the word about the importance of keeping our stormwater clean.
Our Lagoon is a remnant of a tidal slough which was diked and dredged in 1952 to form an enclosed estuary. The Lagoon serves the City as a flood control basin, recreation area, aesthetic amenity, and ecological resource. Lagoon operation and management is centered around optimizing this area so that it can serve these many uses.
Lagoon has experienced a shallowing and sedimentation, which has resulted in hazards and barriers to navigation, reduced stormwater retention, and reduced water quality and circulation. In addition, the shallowing of the Lagoon leads to reduced water flow and increased temperatures which creates an environment for increased nuisance vegetation growth and impacts to water quality.
Moffatt & Nichol, a professional services consultant, provided a preliminary Maintenance Dredging Assessment of the Lagoon in 2018. The assessment included a regulatory review to identify permits needed for future dredging, identification of disposal options, preliminary sediment testing, conceptual level costs for dredging and disposal options, and an updated hydrographic survey to determine current sedimentation levels throughout the Lagoon.
The study estimated that up to 270,000 cubic yards of sediment would need to be removed to restore the Lagoon to its original operating capacity; at a cost of up to $80 million.
Smaller dredge projects at critical areas could be conducted, but none for less than $8 million. Limited disposal options result in a more expensive project. The stormwater capacity for the 100-year flood control criteria is not yet threatened and the Lagoon is still operating as an effective flood control structure. If no dredging takes place, water quality, recreation, and other beneficial uses will continue to be compromised.
Please sign up to receive updates on future dredging discussion. Write to us at email@example.com with your email.
Operation and Maintenance Permits for the Marina Lagoon
Historically, we have been subject to five-year permits from the Army Corp of Engineers (ACOE), California Department of Fish and Wildlife (CDFW), and the Regional Water Quality Control Board (RWQCB) for routine maintenance projects conducted within the Lagoon. Activities covered include oversight of the private dock construction program, sand replenishment at the beaches, fence building, bank stabilization, vegetation harvesting, and limited sediment removal. The current permits expire at the end of 2021; staff is currently in the process of re-applying for these permits. Our plan is to continue to operate and maintain the Lagoon in a similar manner as we have in the past. However, there is a chance that the regulatory agencies could change the requirements or make them more restrictive. Bookmark this webpage for updates.
Our Public Works Department hired a professional consultant to assist with negotiating reasonable permit conditions. To date, several meetings with the regulatory agencies have occurred. Ideally, all final permits will be issued to us by the end of the year, however working with multiple regulatory agencies is often slow and it may take longer. Staff is hopeful that the conditions will be manageable, and that we can continue to provide the same level of service and management of this valuable resource. Dock permitting procedures may need to be modified to incorporate new requirements. Staff will work expeditiously to revise procedures, fees, and guidance so that dock permits can be issued as soon as possible, subject to new permit conditions.
One of staff's challenges with the Lagoon is controlling the aquatic weed and algae growth. With the shallower water, the sunlight now reaches the bottom easily and with warmer temperatures, conditions are ideal for plant growth. Because much of the stormwater runoff from the City flows to the Lagoon, the water is rich in nutrients, adding more fuel for more growth.
In the past, staff used a combination of different herbicides targeting different stages of the growth cycle. Fluridone is typically applied early in the spring before signs of growth emerge – to knock back growth of widgeon grass, which supports the growth of algae. Copper and diquat have been used in the past to treat growth that emerges on the surface.
Herbicide use is strictly monitored and regulated by the State. Due to a product label regulatory change, we can no longer use fluridone for widgeon grass treatments. Copper containing herbicide had been used successfully in the past. However, copper use is severely restricted due to water quality criteria that limit the ability to apply effective concentrations. The availability of alternative herbicides is limited, costs more, and are not as effective.
Due to limited herbicide options, staff turned to a mechanical solution to address the growth by using harvesters. On June 28, 2021, one harvester was deployed to start removing the widgeon grass from areas D, E, and F. On July 8, 2021, a second harvester began operating to assist with the removal. The harvesters are not able to operate in the shallow water at the far south end of the Lagoon. For these areas we are employing an airboat to apply herbicide to growth in these shallow waters. Herbicides have been used for four separate treatment events so far in 2021, treating for both algae and widgeon grass.
Staff has been meeting with the Regional Water Board, the County Ag commissioner, and the herbicide distributor to conduct efficacy trials at the Lagoon for a Special Local Needs registration from the State Department of Pesticide Regulation. This will enable staff to apply fluoridone early on as we have done in the past. If approved, though it will be too late for treating growth this year, it could provide a level of certainty for our options next season.
Aquatic Management Announcements
Stay informed on announcements as they are issued. Not getting announcements? Email us at BHarms@CityofSanMateo.org to add your email to our list.
Unlike our sewer collection and treatment system, we currently do not have a dedicated funding source for dredging or any other stormwater operations, maintenance, or infrastructure renewal activities. All funding is therefore from the City’s General Fund. At the May 17, 2021 City Council study session, staff presented an overview of the stormwater activities, including Lagoon, and a recent Stormwater Funding Analysis performed by SCS Consulting Group.
The analysis is broken into three sections:
- Evaluation of projected financial needs;
- Evaluation of potential funding sources; and
- Preliminary rate structure and recommendations.
The projected operating costs for fiscal year 2022 totaled $3.6 million. Capital costs were estimated at $139 million (including dredging). After amortization of capital costs into a 30-year model, the total annual costs for the hypothetical stormwater utility are $8.4 million.
The analysis identifies various funding sources for a stormwater utility with the most common being a user fee similar to water, sewer and garbage services. The analysis concludes that a user fee of approximately $16 per month for the average residential property could be required to fund the full annual cost. Council directed staff to proceed with conducting community outreach and polling to obtain resident input regarding the potential storm system fee and to better inform potential future ballot measures. That additional scope of work was approved by City Council at its Aug. 16, 2021 meeting. For more information on our Clean Creeks and Flood Protection Initiative, visit the www.cityofsanmateo.org/stormwater webpage.
- What types of recreation are available on the Lagoon?
- We have mosquitoes around the backyard and our boat dock, how can I get help with this?
- Who is responsible for maintaining the water quality of the lagoon?
- What can residents do to help improve water quality of the Lagoon?
- Have any other tips for citizen involvement?
- Why is the water level in the Lagoon low in the winter months and higher in the summer months?