COMMITTEE AGENDA MEMORANDUM
Environmental and Water Resources Committee
Government Code § 84308 Applies: Yes ☐ No ☒
(If “YES” Complete Attachment A - Gov. Code § 84308)
SUBJECT: title
Receive Information on Calabazas and San Tomas Aquino Creek-Marsh Connection Project Staff Recommended Alternative.
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RECOMMENDATION: Recommendation
Receive Information on the Staff Recommended Alternative for Calabazas and San Tomas Aquino Creek-Marsh Connection Project, Project No. 20444001.
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SUMMARY:
Once constructed, the Calabazas and San Tomas Aquino Creek-Marsh Connection Project (Project) will create up to 1,800 acres of wetland within the former A4 and A8 complex salt ponds. For the Project to proceed with the construction phase, funding will need to be identified and secured. The Project is part of the larger South Bay Salt Pond Restoration Project (SBSPRP) and is a partnership between Valley Water and the Don Edwards San Francisco Bay National Wildlife Refuge. The planning and design phases of the project are included in the Capital Improvement Program Five-Year Plan. With funding from the Watersheds Stream Stewardship Fund (Fund 12) and funding from the Environmental Protection Agency (EPA) San Francisco Bay Water Quality Improvement Fund (SFBWQIF), San Francisco Bay Restoration Authority (SFBRA) Measure AA, and the California Department of Fish and Wildlife (CDFW) Proposition 1 (Prop 1) Grant, Valley Water has completed a Planning Study for the Project, which identifies and compares feasible alternatives and recommends a preferred alternative. This memo summarizes the Planning Study and Staff Recommended Alternative.
Background
Historic channelization and other modifications to lower Calabazas and San Tomas Aquino Creeks have disrupted natural sediment transport to the Bay. The transition from managed salt ponds to open water habitat in the adjacent Pond A8 complex presented an opportunity to restore natural tidal and fluvial processes that deposit sediment and form marsh over time. A landscape visioning effort between Valley Water, the San Francisco Estuary Institute, and SBSPRP developed the project concept in 2018, and Valley Water completed a Feasibility Report in 2021. At the April 27, 2021 Board meeting, staff presented the Project scope, which included a preliminary evaluation of Project feasibility. The Project scoping identified three primary objectives: ecological restoration, resilient flood protection through sediment delivery to support marsh formation, and reduced long-term creek maintenance. Three broad implementation options were developed with estimated planning, design, permitting, and construction costs ranging from $6 million to $25 million, and the Board authorized proceeding with a Planning Study to refine alternatives and identify a staff-recommended option. Then, in 2023, the Board approved expanding the Project area to include the Valley Water-owned Pond A4. This expansion increased planning phase costs and duration. Valley Water secured funding for the Planning Study through the following grants:
• SFBRA Measure AA - $3.37 million
• CDFW Prop 1 - $0.5 million
• EPA SFBWQIF - $3.8 million
These funds supported consultant contracts for planning, modeling, and related efforts.
Planning Process
Development of the Planning Study Report was guided by the primary objective: to ecologically restore and enhance the tidal and freshwater marsh and river habitat in the project area. Secondary objectives and/or incidental benefits include sea-level rise resiliency, reduced maintenance in lower Calabazas and San Tomas Aquino Creeks, and public access to the Bay to the maximum extent feasible consistent with the project. A series of public meetings were held to gather input on the Project objectives and alternatives. On May 16, 2023, staff presented conceptual alternatives to the community and on October 24, 2023, a stakeholder meeting was held to gather input on public access features and impacts associated with the Project. A systematic alternatives assessment methodology was then developed through extensive coordination with project partners and regulatory agencies, and focused stakeholder meetings. This structured screening and ranking methodology was used to evaluate restoration designs (including number and location of berm breaches, island habitat features, and active vs. passive creek realignment) against the Project objectives. Hydrodynamic modeling was used to simulate the effects of different breaching scenarios on sediment transport, marsh accretion, and water quality. On May 15, 2024, a public meeting was held to present the results of the feasible alternatives analysis and the preliminary Staff Recommended Alternative (SRA) and gather feedback from the community. Additional modeling was then conducted to assess rates of marsh accretion, flood risk, and water quality changes associated with the preliminary SRA under a range of future scenarios. Extensive water quality, habitat, and species surveys were conducted to establish a baseline for adaptive monitoring and to inform the environmental review and permitting process.
Staff Recommended Alternative
Based on the detailed feasible alternatives analysis, Alternative 6 (Creek Reconnection, Alviso Slough and Pond A4 Breaches) resulted in rapid marsh formation, improved water quality, and reduced creek maintenance in the most cost-effective manner. Key features of this alternative include:
• Connecting Calabazas and San Tomas Aquino Creeks to the A8 Ponds by breaching the inner Pond A8 berm and blocking flows to Guadalupe Slough (does not actively realign San Tomas Aquino Creek).
• Restoring tidal action to the Pond A8 complex through three breaches of the outer levee and removal of the existing water control structure.
• Connecting Sunnyvale East Channel to Pond A4.
• Restoring tidal action to Pond A4 through one breach to Guadalupe Slough.
• Building a vegetated ecotone on the southern edge of Ponds A4 and A8.
• Construction of a one-mile segment of the San Francisco Bay Trail in partnership with the City of San Jose
• Reducing costs by eliminating habitat islands and using passive restoration techniques.
Flood Risk
The Project was designed to reduce flood risk in San Tomas Aquino and Calabazas Creeks by increasing flow velocities and reducing sediment accumulation in the creeks at the 90-degree choke point. In addition, the 1,800 acres of restored tidal marsh act as a natural buffer that can grow vertically by trapping sediment, helping the shoreline keep pace with rising sea levels. The Project creates ecotones, gradual slopes which further buffer the shoreline by allowing marsh habitat to migrate upslope as water levels rise.
Wetland accretion and tidal circulation modeling was used to assess changes in coastal and fluvial floodplains (Calabazas Creek, San Tomas Aquino Creek, and the Guadalupe River) and water levels that result from the Project. Modeling indicates that the increased tidal marsh coupled with the increased tidal storage provided by the pond berm breaches will either reduce flood risk or keep it unchanged across most of the project area. In general, water levels along creeks are expected to be lower and extreme high tide water levels are expected to be lower through most of the project impact area. However, modeling indicated that increased water levels in Pond A4 (which is currently managed to remain at a low water level) may undermine the stability of and/or overtop portions of Pond A4 berm during the 100-year coastal storm event coupled with a 10-year fluvial flood event. Flood risk reduction measures at Pond A4 will be partially implemented as part of the Sunnyvale East/West Channels Flood Protection Project, and Valley Water will evaluate additional potential measures to be included in the Project during the Design Phase.
Water Quality
Previous restoration actions associated with the South Bay Salt Pond Restoration Project between 2011 and 2017 demonstrated that changes in tidal connectivity can mobilize legacy sediment-associated mercury, leading to short-term increases in methylmercury in water and biota. To better understand this risk and project impacts during the post-construction monitoring phase, Valley Water studied current water quality and mercury sedimentation and mobilization conditions in the ponds and sloughs. The study found that mercury was primarily found in sediments, while methylmercury was predominantly dissolved in the water. Additionally, there was significant bioaccumulation of methylmercury in fish.
Project-related short-term increases in turbidity and suspended sediment concentrations in Study Area ponds and sloughs are expected to temporarily increase total mercury and methylmercury concentrations in the water column and subsequently increase the potential for methylmercury uptake in algae, invertebrates, and fish. In the long term, the improved tidal exchange is expected to reduce methylmercury production, and the enhanced sediment deposition is expected to bury the legacy mercury in the ponds. This could improve the bioaccumulation of methylmercury. In addition, improved tidal exchanges should address other water quality concerns, such as reducing algae production and salinity.
Next Steps
Following the Committee's input, staff will finalize the Planning Study Report in June 2026. Project design is expected to begin in July 2026 and will be partially funded by existing grants. Staff will continue to seek grant funding to complete the design and construction of the Project.
ENVIRONMENTAL JUSTICE IMPACT:
The project will benefit surrounding communities, including the Alviso community, by providing habitat restoration, resilient flood protection, reducing invasive creek maintenance activities, and enhancing public access and recreational opportunities.
ATTACHMENTS:
Attachment 1: PowerPoint
UNCLASSIFIED MANAGER:
Manager
Lisa Bankosh, 408-630-2618