Dredging Analysis

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 stormwaterinspectors@cityofsanmateo.org 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 2026; 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.

Vegetation Management

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.

The City's Lagoon vegetation management contractor applies a systemic herbicide Imazamox (Imox) to the Lagoon during Spring and Summer and uses an algaecide GreenClean for localized (spot) treatment for algae. All chemicals used do not pose any threat to wildlife or human health. Aquatic dyes are also used to reduce light penetration through the water column, thereby restricting photosynthesis and constraining plant and algal growth. Mechanical harvesting is another option for vegetation removal if treatments are not effective. 

Aquatic Management Announcements

Stay informed on announcements as they are issued. Not getting announcements? Email us at stormwaterinspectors@cityofsanmateo.org to add your email to our list. 

Funding Analysis

For information on funding for dredging or any other stormwater operations, maintenance, or infrastructure renewal activities, please refer to this link: Community Flood & Storm Protection Initiative

Efforts to Reduce Bacteria Issues

Water quality testing at Marina Lagoon beaches, Lakeshore Park, and Parkside Aquatic has found fecal indicator bacteria (FIB), including E. coli and Enterococcus. The Regional Water Quality Control Board (RWQCB) has determined the water quality at both beaches as impaired for the beneficial uses for water contact (swimming) and non-contact (boating) recreational uses. The bacteria Total Maximum Daily Load (TMDL) amendment to the San Francisco Bay Basin Water Quality Control Plan addresses this FIB issue by requiring the City to submit plan[s] describing Best Management Practices (BMPs) to be implemented to identify potential sources of bacteria to the beaches and reduce their contribution that impairs water quality. The plan includes a methodology for inspecting sewer and storm drain piping to identify and correct any illicit connections or pipe defects needing repair, efforts to reduce potential pet waste, evaluate contributions from wildlife sources, and a schedule with milestones for effective implementation. These related goals are being addressed by implementing the City’s TMDL Implementation Plan, created in 2018.

The City has initiated multiple actions described in our Implementation Plan: 

• Inspection and repair of sewer and storm drain infrastructure citywide as part of the City’s Clean Water Program https://cleanwaterprogramsanmateo.org/
• Detecting and eliminating illicit discharges to the stormwater system and Lagoon. (To report illicit discharges: https://www.cityofsanmateo.org/169/Report-Stormwater-Pollution).
• Pet waste management, including installation of waste bag dispensers at City Parks and Beaches (see how you can help below).
• Goose control program (see how you can help below).
• Illegal dumping complaint/response program.
• Commercial/Industrial business inspection program. 
• Improvements to Private Sewer Lateral Program
• Inspection of docks at the Lagoon
• Public outreach and education.

How You Can Help With Pet Waste Management 

Pet waste is one of the largest contributors to water quality problems in San Mateo County—but it’s one that each of us can help correct. 

1. Bag-it! Always bring plastic bags to pick up after your dog. Don’t forget to throw the bag into a garbage receptacle—leaving bags along trails or in parks is considered littering and is subject to fines. The longer dog waste stays on the ground, the greater the chance for soil and water contamination, so be sure to pick up the droppings promptly! This applies to parks, along trails, and even backyards. BUT, aren’t plastic doggie bags even worse for the environment? NOPE! Runoff carrying untreated dog waste infects our waterways with bacteria that can sicken people and pets, harm aquatic organisms, and contaminate water sources. A landfill is lined and contained.
2. DO NOT COMPOST PET WASTE! Contrary to popular belief, dog waste is not recommended as a natural lawn fertilizer. While animal manure can in some cases and under carefully managed conditions, make useful fertilizer, parasites carried in dog and cat feces can cause diseases in humans and should not be incorporated into compost piles.
3. Don’t forget about your other pets! Make sure to clean up after your dogs, cats, horses, and other household pets. Help keep our waterways and communities clean!

How You Can Help With Goose Control 

Goose poop is a major contributor of FIB in the Lagoon. Geese tend to congregate in areas where they have been fed by people. So please remember: