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Dredging Umbrella Permits

In December 2022, the US Army Corps of Engineers (USACE) contracted with The Dutra Group to complete a full dredge of the San Rafael Channel.

The USACE is only responsible for dredging the Federal Channel (which does not extend to private docks and marinas). Private property owners are responsible for dredging from their private docks up to the Federal Channel which is in the center of the Canal.

However, since the USACE provided for the majority of mobilization of the dredging contractor, it proved to be cost effective for waterfront property owners to have their private docks dredged by the USACE contractor, The Dutra Group, in conjunction with the USACE Federal Channel dredging.

Property owners who signed up with the City's private dredging effort will receive permits that have been secured on their behalf from several regulatory agencies by the City of San Rafael. Those "umbrella permits" will be pursuant to  an agreement with the City of San Rafael that will ensure the proper testing, permitting, reporting, review and approval by various SF Bay regulatory agencies for each proposed dredging operation proposal.

Please note: the following information will be needed to dredge under the City’s umbrella permit, under no circumstances will dredging be permitted under the City’s umbrella permit without a completed permit application and agreement. 

Dockowners who participated in the City's umbrella permitting project must follow the steps below to prior to each episodic dredge operation:

  1. City of San Rafael Tidelands permit application, $15,000 tideland permit fee and agreement: this will include a fairly detailed project description, complete with new soundings or a bathymetric survey and a volume estimate (City staff can work with your dredging contractor to calculate the volume estimate), and a drawing of the proposed dredging area. This must be located within the confines of your permitted dredge footprint. The Tidelands application and agreement are required prior to any dredging activity on your parcel. All dredging operations plans and activities must be compliant with the San Francisco Maintenance Dredger’s handbook, as well as with each regulatory permit secured on your behalf.
  2. Upon receipt of a success tidelands permit application, the City will prepare a Tier I sediment quality evaluation and present it to the Dredged Materials Management Office.
  3. Upon a successful approval from the DMMO of the sediment quality, you (or your designated dredging contractor) will prepare a Dredge Operations Plan that City staff will review and submit to the DMMO if it is deemed adequate.
  4. Once dredging is completed, a final report must be submitted by the applicant/dredging contractor. City staff will review and submit to the DMMO once it is deemed adequate.
  5. For dock owners located in upper reaches of Canal with contaminated material: If a dockowner from Reach 4 wants to consider in-Bay disposal instead of ocean disposal, additional sediment testing will be required that will be , and they would contract that separately. If they do that through another firm, we would need to review the SAP and the final reports prior to submission to the DMMO.
  6. After three years, all dockowners will need to conduct some level of testing regardless of disposal option, and #4 would apply.

To minimize adverse environmental impacts and the unpermitted deposition, spill, or discharge of any liquid or solid into the sea, the applicant shall implement the following requirements and best management practices described in the ‘Dredger’s Handbook: A testing, permitting, and reporting guide for maintenance dredging in the San Francisco Bay – January 2021’ and will abide by all construction, testing, permitting, and reporting requirements of the handbook  at a minimum, in addition to the requirements of all aforementioned permits secured under the umbrella permitting process.

What does the $15,000 permit fee pay for? 

Because the City of San Rafael does not have a dredging and regulatory consultant in-house, we must contract professional services required to administer all permits under the City's umbrella permits. The services provided for the $15,000 fee include the following:

  • Evaluation of the proposed project description to ensure consistency with the 10-year permits.
  • Confirmation of proposed dredging volumes.
  • Preparation of engineering plans for inclusion in the episode approval request and the dredge operations plan.
  • Preparation of the episode approval document, which includes the following:
    • An assessment and quantification of any additional shoaling
    • An evaluation of available sediment quality data
    • Review and compilation of any project area spills or discharges that have been added to the State spill database
    • Presentation of the episode approval document to the five DMMO agencies
  • Review and approval of the contractor Dredge Operations Plan for compliance with the 10-year permits
  • Review of the final dredge report for compliance with the 10-year permits

For further questions on the umbrella permitting process, contact Scott Bodensteiner of Haley & Aldrich at

Umbrella Permits FAQ's

During the initial permit acquisition process you will be asked to provide information about your property. It is not anticipated that additional involvement in the permitting process beyond the initial information gathering phase will be necessary.

You may apply as a tenant, however you will ultimately need the permission of the property owner as would be the case with any other property renovation.

Yes, but you will have to navigate the permitting process on your own, and you will not be able to take advantage of the substantially discounted group rate for permits under the Umbrella Permitting process.

The City of San Rafael will be listed as the permitee.

For the permitting process, the participating property owners/tenants will also be responsible (and pay an equal portion) for the cost of retaining a specialized consultant to manage the process. For the dredging, each participating property owner/tenant will contribute a portion of the total fee based on the volume of material present above the target dredge depth in their property’s dredge area.

The City of San Rafael does not have dredging permitting expertise on staff, as the process is something the City has engaged in only twice in the past 25 years. A firm with expertise facilitating the maintenance dredging permitting process is necessary to ensure all permits and approvals are in place when the USACE initiates their dredging project. The cost of retaining the firm will be equally split between dock owners/tenants which participate in the Umbrella Permitting process.

Once approved, maintenance dredging permits are good for 10 years.

Yes, you may not perform dredging operations in and around a private dock without a valid permit.

Yes, the City and the firm will follow up with participating dock owners/tenants at a later date once the USACE dredging contract has been awarded.

The permitting process will take approximately one year.

You may contact Scott Bodensteiner, Program Manager with Haley & Aldrich at

It would be advisable to review your current permits to determine when they expire. If there are still three or more years on the permit, then, assuming the USACE initiates the federal channel dredging within three years, you will not need a new permit through the Umbrella Permitting process. Those permits can be used to participate in the umbrella dredging episode to be performed in conjunction with the USACE dredging. If your individual permits expire in less than three years and you choose to not participate in the Umbrella Permitting process, then you may have an expired permit and unable to dredge at the time of the USACE dredge episode.

The permitting agencies include the U.S. Army Corps of Engineers (USACE), the San Francisco Bay Conservation and Development Commission (BCDC), the Regional Water Quality Control Board, California Fish and Wildlife, and the City of San Rafael.

The primary maintenance dredging permits to be acquired under the umbrella permit process are good for 10 years, so a delay in USACE funding will not require significantly more expenditures. Renewal of the City permits may be necessary, but this will not require significant effort.

The umbrella permitting cost will be dependent on the number of dredgees. The permitting process will include the acquisition of all permits PLUS the sediment quality approval. The future umbrella DREDGE CONTRACTOR cost will be based on the amount of dredge material and will be split between between all permitted dredgees.

There is a pro in this approach if a HOA or property owner wants to undertake the dredging on their own without piggybacking on the Corps dredging of the federal channel with the other dock owners on the Canal.

If a dredging contractor was doing your dredging independently, they would probably do the permitting at a lower cost. However, this also comes with the con that assumes a stand alone project would result in a higher cost for the dredging (due to mobilization costs) compared to the shared cost of piggyback dredging, so presumably the overall cost would be higher than the City’s umbrella approach. The other con is that due to a number of new regulatory requirements, the permit acquisition process in now more complicated than it was in 2012. Dredging contractors often specialize in dredging whereas the City’s umbrella permitting consultant (Haley & Aldrich) specializes in understanding the regulator expectations and the permitting process. The technical aspects of the sediment quality approval necessary under the permits will also be different and more challenging now too.

The City is working with the USACE so that the dock owners can “piggyback” on the main channel project using the same contractor that the USACE uses, which will result in both scale savings and savings associated with the elimination of mobilization cost.

Yes. The City is working with the USACE so that the dock owners can “piggyback” on the main channel project using the same contractor that the USACE uses, which will result in both scale savings and savings associated with the elimination of mobilization cost.

The USACE pulls their own permits, but will rely on a consultant for their sediment quality approval. They have not selected that consultant yet.

The City wanted to start the permit process now so that dock owners would be cleared to dredge when the USACE started. The FY2021 Work Plan began on Oct. 1. It is still not clear whether they will have funding available after the Work Plan’s priority projects (i.e. Oakland and Richmond Harbors) are completed. If they do have funding for the Canal in 2021, they would dredge the dock owners immediately afterward (same year), and potentially simultaneously as they work their way down the Canal. So there is still potential for the dredging to occur in 2021 although likely it will be in 2022. Either way it would be difficult (probably impossible) to get an individual dock owner added to the permit after the USACE hires a contractor in time for them to be included with the “piggyback” dredging. Docks attached to homes that come under new ownership would stay permitted. The new owners would simply have to sign an affidavit indicating they want to remain on the permits.

Permit acquisition would not be affected by any detected contamination, but the sediment quality approval required by the permits would be. Yes, any homeowners near areas in the main channel that the USACE testing shows to be contaminated would be responsible for additional testing near the dock that would hopefully show the contamination does not extend to the dock dredge area. In this scenario, the strategy would be to test for just the contaminant identified by the USACE testing so that the individual homeowner testing cost would be minimized (1 or 2 contaminants vs. the 158 contaminants required for stand-alone projects).

That is correct. The sediment quality approval process under the umbrella permit would take advantage of a testing exemption allowed for in the EPA guidelines that allows for a report to filed referencing the USACE testing results. This exemption report is included in the umbrella permit cost. However, if USACE finds contamination in the main channel near a residential dock, then some testing would be needed.

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