Zone 5

Area: 40,390 acres
Natural Creeks: 55 miles
Earth Channels: 4 miles
Concrete Channels: 11 miles
Underground Pipes: 49 miles
Improved Creeks: 2 miles

Location: Fremont, Union Pacific Railroad crossing (downstream) to BART weir (upstream)
Anticipated Completion: Phases 1 and 2 – Fall 2028; Phase 3 – Fall 2030

The Lower Alameda Creek channel was designed by the U.S. Army Corps of Engineers in 1955 as a trapezoidal flood control channel. The original design, however, did not account for the significant sediment load carried down from the upper watershed. As a result, the lower sections of the creek have experienced substantial sedimentation. The situation has been further complicated by the presence of sensitive habitats, including fish passage areas. These environmental constraints have made dredging activities increasingly costly and environmentally challenging, requiring extensive mitigation measures.

In response to these challenges, the District has undertaken comprehensive studies to develop a more sustainable long-term solution. The proposed restoration aims to facilitate natural sediment transport through the channel, maintain flood control capacity, improve fish passage and habitat, and maintain the creek’s flood control capacity.

The project is divided into three phases, all of which have secured funding. The majority of construction funding is provided by the State through the Department of Water Resources. Combined with local matching funds (including a portion from Alameda County Water District), the project is fully funded across three construction phases, with an estimated total construction cost of approximately $68 million.

Phase 1 extends from the BART weir to Rubber Dam No. 2, while Phase 2 continues downstream to the Dry Creek confluence. Phase 3 spans from upstream of Decoto Road to just upstream of the Union Pacific Railroad (UPRR) crossing, and includes some overlap and refinement of the lower Phase 2 channel to better align final low-flow channel grades between phases.

Construction for Phases 1 and 2 is scheduled over two construction seasons (May through October) in 2027 and 2028. Site access will be via the north levee, with staging areas located at key points along the levee crest. To complete Phases 1 and 2, approximately 165,000 cubic yards of material will be excavated from the channel. In addition, three bridges will be retrofitted with anti-scour features, the foundation of an abandoned diversion dam (RD2) and four existing rock grade control sills will be modified to improve fish passage. Following advertisement of Phases 1 and 2 for construction bids, engineering and environmental permitting for Phase 3 will commence.

Location: Fremont, San Francisco Bay to seven miles upstream
Anticipated Completion: Study Ongoing

Alameda Creek is one of the largest drainage watersheds in the San Francisco Bay Area, covering nearly 700 square miles and carrying stormwater into the San Francisco Bay. The creek plays a critical role in protecting nearby communities from flooding while also serving as a habitat and passage corridor for native fish species.

To reduce flood risk, major flood control infrastructure was constructed along Alameda Creek beginning in the 1970s. While these improvements helped protect surrounding communities, they also changed how sediment moves through the creek. Today, the lower (downstream) seven miles of Alameda Creek experience significant sediment accumulation. The lowest four miles (starting from the bay) are tidally influenced, and the sediment is probably of tidal origin. The next three miles (upstream of the lowest four miles) accumulate sediment from the upper watershed. This three-mile section has been dredged to remove silt—known as desilting—several times since the channel was constructed. Desilting is very expensive.

A partial solution to sediment buildup along the lower four miles of Alameda Creek near the bay is tied to the South Bay Salt Pond Restoration Project. The District is helping to restore approximately 5,500 acres of Eden Landing salt ponds along the shorelines of Hayward, Fremont, and Union City. A small portion of the north levee is planned to be removed from the lower reach of Alameda Creek near San Francisco Bay to help transfer of sediment from Alameda Creek into the salt ponds. When the levee is opened, bay tides will flow in and out of the lower segment of Alameda Creek and flush out—or “scour”—sediment from the creek. This will significantly increase the channel’s ability to carry stormwater. It will also save millions of dollars in dredging costs and environmental mitigation that it would otherwise incur to remove sediment deposits.

Location: Fremont
Anticipated Completion: 2026/2027

After years of regional collaboration, Alameda Creek now has key fish passage improvements that help steelhead trout, Chinook salmon, and other native fish move upstream and downstream more safely. Steelhead and salmon are born in freshwater, migrate to the ocean, and return to their home streams to spawn, so reconnecting this habitat is critical to their long-term success.

To support that migration while maintaining local water supply reliability, agency partners including the Alameda County Flood Control District, Alameda County Water District, and San Francisco Public Utilities Commission advanced a series of improvements along lower Alameda Creek, including fish ladders and related facilities. The fish ladder at the BART weir and the ladder at Rubber Dam No. 3 are both complete, and recent monitoring shows that multiple species and life stages of interest are successfully using them.

Severe storm events in December 2022 and January 2023 resulted in significant sediment accumulation within the concrete fish ladder structure and resting pool. The buildup has substantially reduced the capacity of these structures and is impeding fish migration to upstream habitats.

In winter of 2025, Chinook salmon were spotted in the Niles Canyon stretch of Alameda Creek for the first time in 70 years. 

To maintain the functionality of the fish ladder at the BART Weir, the District has secured environmental permits to remove the accumulated sediment and restore the capacity of the fish ladder and resting pool, thereby ensuring continued safe upstream migration for fish species.

Location: Union City (approximately 630 ft. downstream of Railroad Ave.)
Anticipated Completion: 2026/2027

Dry Creek was constructed in 1959 to convey stormwater runoff to Alameda Creek, providing flood protection for the surrounding area. Within the project site, Dry Creek is a trapezoidal earthen channel that has experienced progressive bank erosion over time, necessitating stabilization and restoration.

The project will repair approximately 275 linear feet of eroded channel bank to prevent further degradation and restore the creek to its original design section. The restored channel will maintain its capacity to convey 100-year design storm flows. Overall, the project will extend the service life of the District’s flood control facility.

Location: Union City
Anticipated Completion: 2026

Low-lying communities along the San Francisco Bay rely on pump stations to move stormwater from neighborhoods to nearby waterways. The District operates dozens of pump stations across western Alameda County, making them critical assets for managing stormwater runoff and reducing flood risk during heavy storms and the rainy season.

Upgrades and rehabilitation are underway at two pump stations to extend their service life and improve reliability, including the J-2 and J-3 Pump Stations.

A recent study found that key electrical components, generator systems, flap gates, and outfall structures at these facilities are nearing the end of their service life and require upgrades or replacement. Planned improvements include replacement of the generator set, motor control center, automatic transfer switch, transformer, utility metering panels, panelboards, conductors, grounding systems, raceways, and indoor lighting with energy-efficient LEDs.

At the J-2 Pump Station, work will also include rehabilitating and recoating four existing flap gates, replacing two flap gates, lining one discharge pipe, and repairing the deteriorated concrete outfall structure.

At the J-3 Pump Station, improvements will include replacing six flap gates, repairing the deteriorated concrete outfall structure, and recoating pump station piping. Corrosion protection will be applied to flap gates at both stations.

Location: Newark
Year Completed: 2025

The Naturalization of Line D (New Ohlone Creek) represents an innovative and sustainable approach to flood control. It transforms a conventional, man-made trapezoidal flood control channel into a dynamic, natural floodplain system. Line D was originally constructed in 1958 as a single-objective earthen channel. However, that straight line channel experienced repeated bank failures, and in its quest to find a more permanent solution than patch riprap repairs, the Alameda County Flood Control and Water Conservation District (the District) sought a more environmentally sustainable solution. With vacant land belonging to the Ohlone Community College District (OCC) immediately northwest of the channel, it seemed like there might be an opportunity for a creative solution. And, with the adjacent OCC campus hosting the College’s environmental program, the project provides opportunities for students to learn more about natural systems.

The project reimagined the flood control channel as a New Ohlone Creek, a meandering creek traversing a broad floodplain. This design leverages principles of fluvial geomorphology to create a natural equilibrium channel that can adapt to changes in climate and watershed conditions. 

The Flood Control District began discussion with OCC on the naturalization concept, including its synergy with the College’s Environmental Studies program. OCC welcomed the idea and subsequently granted a permanent easement to the District for the implementation of the naturalization project. The District applied for grant funding from the California Natural Resources Agency’s Urban Flood Protection Grant Program, and was awarded $5.9 million towards construction of the project. The estimated total project cost at the time of application was about $8.3M.

Key innovative features of the project include: 

• Natural Infrastructure: The project replaces the existing rock lined trapezoidal channel with a meandering low flow channel and floodplain terraces, promoting natural processes such as sediment transport and infiltration.
• Ecological Benefits: The design supports a native riparian corridor, creating approximately 7 acres of protected floodplain terraces, wetlands, and upland wildlife habitats. This enhances biodiversity and provides critical habitat for various species.
• Community and Educational Benefits: Ohlone College Newark Campus, located adjacent to the project site, will gain opportunities for environmental education and hands-on restoration experiences for students. The project also accommodates plans for future water service passing through the project site to new development, and provides for a future public access trail connecting to the San Francisco Bay Trail and providing recreational opportunities for the community.
• Climate Adaptation: The project design allows the channel and riparian corridor to adapt to changing climate conditions, providing resilience against increased flood frequencies and sea level rise. The riparian vegetation will sequester carbon and reduce greenhouse gases.
• Partnerships: Ohlone Community College District (OCC) granted an easement across 6.9 acres of its land for the project. The District removed 3,900 cubic yards of OCC’s pesticide-contaminated soils and coordinated with Department of Toxic Substances Control (DTSC) on removal and associated documents. The District coordinated with Alameda County Water District to accommodate future domestic water service needs that would need to cross the easement property, including providing brackets for a future water pipeline to cross the new creek on the new bridge. The District is partnering with the Ohlone College professors on access and educational opportunities for students at the Newark campus.

An Operations and Maintenance (O&M) Plan is being prepared to guide ongoing County maintenance work after the three-year contractor maintenance period is over. As an additional means of educating the public and improving relations, an interpretive sign describing the project and its many benefits will be installed at the upstream end of the project alongside the sidewalk at Cherry Street.