Dredging Operation 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.

All dredging projects in waters of the United States require a 401 Water Quality Certification from the Water Board. Permit applications can be found at the Dredged Material Management Office (DMMO) website. The process to receive a permit from the Water Board and other regulatory entities takes approximately 1 year. Please refer to the DMMO tab for more information about that program.

There are many entities which dredge in San Francisco Bay in order to allow safe movement of cargo ships, ferries, and other vessels. The U.S. Army Corps of Engineers conducts the majority of dredging in San Francisco Bay and most of their dredging projects are regulated via the maintenance dredging permit linked below. This permit regulates all maintenance dredging performed within Federal Navigation Channels.

Maintenance Dredging of the Federal Navigation Channels in San Francisco Bay

UPDATE 2/13/2024
As the lead agency under CEQA, the Water Board is seeking comments on the Notice of Preparation for a draft Environmental Assessment / Environmental Impact Report for continued Operations and Maintenance Dredging by the U.S. Army Corps of Engineers. The NOP comment period closes March 14, 2024 at 5:00 pm. A hybrid CEQA scoping meeting will be held on Tuesday, March 5, 4:00 – 6:00 pm both online and at the Water Board’s office. See the NOP below for more detail.

Long-Term Management Strategy (LTMS) for the Placement of Dredged Material in San Francisco Bay

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

Dredged Material Management Office

Water Board staff actively participate in the Dredged Material Management Office (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 ocean disposal site, 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.

Pre-Filing Meeting Request

The 401 Certification Rule requires prospective dredgers to submit a Pre-Filing Meeting Request a minimum of 30 days prior to submitting a Consolidated Dredging-Dredged Material Reuse/Disposal application.

To facilitate discussions on the timing for permit issuance and request requirements, please provide us advance notice (rb2-dredgereports@waterboards.ca.gov) of upcoming permitting requests ahead of receiving the Prefiling Meeting Request.

We are recommending the following schedule for submitting the Pre-Filing Meeting Request Form to ensure we can issue a permit in a timely manner:

Type of Certification¹

When to Submit Pre-Filing Meeting Request

  Single Episode Maintenance Dredging
  Requiring a Sampling and Analysis Plan

  With the Sampling and Analysis Plan,
  when submitted to the DMMO
  Multi-Episode Maintenance Dredging
  with a First Episode Approval		   With the Sampling and Analysis Plan,
  when submitted to the DMMO
  Single Episode Maintenance Dredging
  Requiring a Tier 1 Analysis		   After submittal of a Tier 1 Analysis request to the DMMO,
  submit by email (rb2-dredgereports@waterboards.ca.gov)
  Single Episode Maintenance Dredging
  Requiring a Tier 1 Analysis with
  Confirmatory Chemistry		   After submittal of a Tier 1 Analysis request to the DMMO,
  submit by email (rb2-dredgereports@waterboards.ca.gov)
  Multi-Episode Maintenance Dredging
  Without a First Episode Approval		   After the applicant knows all the information
  needed in the consolidated application and has received an
  integrated alternatives analysis or equivalent document
  approved by LTMS², submit by
  email (rb2-dredgereports@waterboards.ca.gov
  New Dredging Work   After the applicant knows all the information needed in the
  consolidated application, has an integrated alternatives
  analysis or equivalent document approved by LTMS2 and
  has a plan describing avoidance, minimization and
  compensatory mitigation measures, submit by
  email (rb2-dredgereports@waterboards.ca.gov

¹The Water Board is a member of the Dredged Materials Management Office (DMMO). The DMMO is a joint program of the San Francisco Bay Conservation and Development Commission, San Francisco Bay Regional Water Quality Control Board, California State Lands Commission, the San Francisco District U.S. Army Corps of Engineers, and Region 9 of the U.S. Environmental Protection Agency, the California Department of Fish and Wildlife, the National Marine Fisheries Service, and the U.S. Fish and Wildlife Service. The DMMO cooperatively reviews sediment quality sampling plans, analyze the results of sediment quality testing, and make suitability determinations for material proposed for disposal or beneficial reuse in and around the San Francisco Bay area. The DMMO published the Dredger’s Handbook – A Testing, Permitting, and Reporting Guide for Maintenance Dredging in the San Francisco Bay (Handbook). Prospective dredgers should become familiar with the Handbook to facilitate the permitting process and various dredging terms for the prospective project.

²The Long-Term Management Strategy for the Placement of Dredged Material in San Francisco Bay (LTMS) Program Managers are responsible for reviewing and approving plans that explore alternative dredged material placement sites under the Clean Water Act 404(b)(1) Guidelines.

401 Request Requirements

The Water Board will continue to accept the Consolidated Dredging-Dredged Material Reuse/Disposal application as a request for 401 certification. The Consolidated Dredging-Dredged Material Reuse/Disposal application may be submitted 30 days after submitting the Pre-Filing Meeting request. Ahead of submitting the application/request, confer with the project’s Program Manager on the project’s readiness for 401 certification.

Please ensure that the Consolidated Dredging-Dredged Material Reuse/Disposal application package contains all of the following requirements for a request for 401 certification pursuant to 40 CFR Part 121:

  1. Identify the project proponent(s) and a point of contact;
  2. Identify the proposed project;
  3. Identify the applicable federal license or permit;
  4. Identify the location and nature of any potential discharge that may result from the proposed project and the location of receiving waters;
  5. Include a description of any methods and means proposed to monitor the discharge and the equipment or measures planned to treat, control, or manage the discharge;
  6. Include a list of all other federal, interstate, tribal, state, territorial, or local agency authorizations required for the proposed project, including all approvals or denials already received;
  7. Include documentation that a prefiling meeting request was submitted to the certifying authority at least 30 days prior to submitting the certification request;
  8. Contain the following statement: “The project proponent hereby certifies that all information contained herein is true, accurate, and complete, to the best of my knowledge and belief”; and
  9. Contain the following statement: “The project proponent hereby requests that the certifying authority review and take action on this CWA 401 certification request within the applicable reasonable period of time.”

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 half of the average annual pre-2000 in-Bay disposal volume.

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 (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.

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.

To learn more about Beneficial Reuse click on this link.

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