Dredging Operations and Sediment Management

Any dredging and disposal activity in San Francisco Bay, marshes and creeks requires a permit from the Water Board. The Water Board works with its federal, state, and local partners in the Long Term Management Strategy for the Placement of Dredged Material in the San Francisco Bay Region (LTMS) to manage navigational dredging and disposal activities in the Bay Area. The navigational dredging program is included in the Basin Plan's Implementation Program.


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Maintenance Dredging of the Federal Navigation Channels in San Francisco Bay

LTMS Program

In 1990, the State Water Board, the SF Bay Regional Water Board, the Bay Conservation and Development Commission, the U.S. Environmental Protection Agency, the U.S. Army Corps of Engineers, and the State Lands Commission created the LTMS Program, a collaborative partnership involving regulatory agencies, resource agencies, and stakeholders working together to address potential impacts from dredging and dredged material disposal to water quality, wildlife, and beneficial uses of the Bay. The LTMS Program has four main goals:

  • Maintain in an economically and environmentally sound manner those channels necessary for navigation in San Francisco Bay and Estuary*;
  • Conduct dredged material disposal in the most environmentally sound manner;
  • Maximize the use of dredged material as a resource; and
  • Establish a cooperative permitting framework for dredging and disposal applications.

*Includes tidally influenced portions of Bay tributaries

LTMS 12-Year Review

The LTMS Management Plan, adopted in 2001, called for reducing aquatic disposal in the Bay using four three-year “step-down” periods that ended in 2012. Starting in 2013, in-Bay disposal of dredged material is limited to 1.25 million cubic yards (mcy) per year, which is approximately 52 percent of the average annual pre-2000 in-Bay disposal volume (calculated using disposal volume data from 1991 to 1999).
The Management Plan also called for periodic review and/or modification to ensure that the program remains achievable and current in light of changing conditions over time. In 2013, in addition to completing the transition to substantially reduce in-Bay dredged material disposal, the LTMS agencies also completed a comprehensive 12-year review of the program. The review process involved collecting, analyzing, disseminating, and presenting data about the program’s performance as well as a series of public meetings (each focused on a different key topic suggested by stakeholders) and preparation of a Final 12-Year Review Report summarizing the review findings. The 12-Year Review Final Report was issued in August 2013. The most significant findings include:

  • Reduced in-Bay Disposal. The in-Bay disposal volume reduction targets were successfully met for each 3-year increment of the transition period between 2000 and 2012. Approximately 48 mcy were dredged from the Bay between 2000 and 2012, of which 19 mcy were placed at in-Bay sites (39% of the total volume dredged), 21 mcy were placed at beneficial reuse sites (44% of the total volume dredged), and 8 mcy were placed at the San Francisco Deep Ocean Disposal Site (SF-DODS) (17% of the total volume dredged).
  • Increased Beneficial Reuse. The beneficial reuse of 44 percent of the total volume of sediment dredged from the Bay during the 12-year transition period is a significant accomplishment.  Most of this material came from USACE channel deepening projects and was placed at a few large habitat restoration sites.  Substantial capacity for beneficial reuse still exists, but the distance of beneficial reuse sites from the majority of the dredging activity and the need for dredging projects to provide offloading equipment at certain sites remain challenges in providing economical reuse options.
  • Changed Conditions. The LTMS agencies considered whether a change to the program was needed to address increasing sea levels and a reduced sediment supply from the Delta. The agencies concluded that the goal of maximizing beneficial reuse of dredged sediment remains appropriate and is even more important now than it was in the early days of the LTMS program. Dredged sediment placement at tidal marsh restoration sites raises elevations and increases the rate at which vegetation colonizes, making these sites more adaptable to sea level rise. Disposing of clean sediment in the ocean is less desirable now because it results in the permanent loss of sediment from the Bay system.

Dredged Material Management Office (DMMO)

Water Board staff actively participate in the DMMO, which was created as part of the LTMS Program to provide a “one-stop shop” for processing applications for dredging and disposal projects in the San Francisco Bay region. The DMMO cooperatively reviews sediment quality sampling plans, analyzes the results of sediment quality sampling, makes suitability determinations for disposal, offers a consolidated application that can be jointly processed for each agency’s permits for dredging and disposal projects in San Francisco Bay, the SFDODS, and beneficial reuse sites. The goal of this interagency group is to increase efficiency and coordination between the member agencies and to foster a comprehensive and consolidated approach to handling dredged material management issues.

Beneficial Reuse and Sea Level Rise Adaptation

Beneficial reuse of dredged material is an integral and necessary part of the dredged material management process, especially in light of the 1.0 to 2.4 feet of sea level rise expected in San Francisco Bay by 2100 (Water Board 2019). Dredged material can be beneficially used in upland, wetland, and aquatic environments. More details, plus a map showing the locations of active and soon-to-be active beneficial reuse sites around the Bay, are available here.

San Francisco Estuary Institute (SFEI) maintains a database called Sedimatch to help the dredging community connect with projects in need of clean sediment. Guidelines for physical, chemical, and biological sediment testing and evaluation of test results for placement of dredged materials in beneficial reuse environments are available in this document.

Port of Oakland Harbor Navigation Improvement (-50 Foot) Project and Beneficial Reuse

January 2010 marked the completion of the delivery and beneficial reuse of dredged material from deepening the Oakland Harbor, a 10-year process conducted under a series of permits issued by the Water Board.  Beginning in 2002, over 12 mcy of sediment was dredged to accommodate new classes of container ships.  Permits issued by the Water Board protected human health, habitat, and water quality during both the dredging and the subsequent relocation of the dredged material.  Nearly 100 percent of the dredged material from the Oakland Harbor has been reused for wetland restoration, habitat enhancement, and construction projects in and around the San Francisco Bay.

One of the first areas in the San Francisco Bay region to realize the benefits of reusing dredged material from the Oakland Harbor was Middle Harbor Shoreline Park, adjacent to the Port of Oakland.  Approximately 5.8 mcy of dredged material is being used to restore about 188 acres of shallow water habitat, such as eelgrass beds, and to provide recreational access to the Bay at a location previously cut off from such access.

Hamilton Wetlands Restoration Project

This project is a joint effort of the Army Corps of Engineers and the State Coastal Conservancy that is restoring approximately 640 acres of tidal wetlands, seasonal wetlands, transitional zones, and upland habitats. The restored wetlands were formerly runways and grassland areas at the former Hamilton Army Airfield in Novato. Hamilton/Bel Marin Keys Wetlands Restoration website.

Approximately 6 million cubic yards of sediment have been placed at the site (see photos above) to create and restore the proper elevations for tidal and seasonal wetlands. This project is similar to a few other projects in the Bay that have demonstrated beneficial reuse of dredged sediments, for example, Sonoma Baylands.  This project is a major contribution to the restoration of priority habitats for San Pablo Bay.  After many years of remediation and restoration work, the wetlands were opened to tidal action on April 25, 2015. The restored wetland will provide ecological benefits for several endangered and other target species such as California clapper rail, Chinook salmon, steelhead, salt marsh harvest mouse, shorebirds and others. The Army Corps will conduct monitoring and adaptive management at the site for 13 years post-breach in order to ensure that the restoration goals are met. After this period, the State Coastal Conservancy will continue to monitor the development of the wetlands and maintain the site.

Montezuma Wetlands Restoration Project

This privately owned and operated project located at the eastern edge of the Suisun Marsh will restore nearly 2,000 acres of tidal and seasonal wetlands on historical tidal marsh land that was diked and drained for agricultural use more than 100 years ago. Since opening in December 2003 and through 2019, Montezuma has received approximately 8 mcy of dredged material out of a total of 17.5 mcy available. A substantial portion of dredged sediment, 3 mcy, came from the Oakland Harbor Deepening Project. This project is unique because some of its dredged material placement cells are designed and constructed to contain sediment that is slightly more chemically challenged than the cleanest Bay sediment that is typically used in tidal marsh restoration projects.  This type of sediment is called “foundation” or “noncover” material to differentiate it from “surface” or “cover” material. Up to 20% of the dredged material delivered to the project may be foundation material. The Water Board’s permit requires that foundation material must be covered by, at a minimum, three feet of surface/cover quality sediment and be isolated surface-water bodies and constructed channels by at least 200 lateral feet of surface sediment. Acceptance of foundation material allows beneficial reuse of sediment that would otherwise be permanently lost from the Bay system via disposal at SF-DODS or upland sites.