The 660-square-mile Alameda Creek Watershed is the largest watershed in the Bay Area. It extends as far south as Mount Hamilton, north to Mount Diablo, east to the Altamont Hills in Livermore, and west to San Francisco Bay. The information in this watershed page focuses on the Lower Alameda Creek Watershed. This portion of the watershed makes up just 6 percent of the total watershed area and is located in western Alameda County within the Alameda County Flood Control and Water Conservation District’s (the District) jurisdiction. This 41-square-mile portion includes the Walpert Ridge area of the East Bay hills and the flatlands of Fremont and Union City. The flatlands were created by Alameda Creek itself, each successive flood laying down another layer of sand, silt, and gravel to form a large alluvial fan that slopes gently bayward.
Overview Map (click to expand)
Lower Alameda Creek Watershed Map (click to expand)
Downloads: Overview map (PDF) | Lower Alameda Creek Watershed map (PDF)


Eden Landing Salt Ponds

Flora and Fauna

The Agua Fria Watershed drains the Diablo Ridge across grassland hills where cattle graze under the occasional coast live oak, valley oak, blue oak, Mexican elderberry, and Pacific madrone. Common trees in the riparian corridors include white alder, California sycamore, and willow. California poppies, monkey flowers, and lupines are prevalent wildflowers during the spring. The East Bay Regional Park District publishes a wild plant checklist for all plants found within Mission Peak Regional Preserve located in the watershed. Many small mammals and a population of coyotes inhabit the Mission Peak ridgeline area. The Diablo Range garter snake, which closely resembles the California garter snake, is also common.The Agua Fria drainage flows into Coyote Creek, which, from aerial photos of south San Francisco Bay, appears as the longest of several twisted tendrils extending inland through a maze of salt ponds and restored tidal marsh. The marsh plain is part of the Don Edwards San Francisco Bay National Wildlife Refuge—home to nesting shorebirds as well as 45,000-75,000 migrating waterfowl. Two reports provide specific details on San Francisco Bay salt pond and tidal marsh habitats: a policy background report from the San Francisco Bay Conservation and Development Commission; and from the San Francisco Estuary Project, a habitat assessment as part of a bay-wide collaborative effort to identify habitat goals.

Geology and Hydrology

The Agua Fria Watershed drains through Miocene epoch sedimentary rock on the west side of the Diablo Ridge and then through Pleistocene epoch sediments to I-680. The drainage is directed into culverts under I-680, which parallels the Hayward Fault. During the Pleistocene epoch, a large river flowed through this area to what is now south San Francisco Bay. Movement along the Hayward Fault interrupted the river flow, creating many creeks. In the last several thousand years, these creeks flowed to the bay across a wide marsh plain thick with vegetation and branching waterways. The process that formed south San Francisco Bay tidal marshes is explained in detail in the Mowry Slough section.

Major Issues

Water contamination levels in the Agua Fria Watershed are consistent with urban areas in the region. Mercury, PCBs, and PBDEs are the greatest concerns, while dioxins, pyrethroids, PAHs, and selenium are also problematic. Though overwhelming evidence demonstrates the potential of tidal marshes to improve water quality, the large-scale restoration activities in the South Bay may have their own adverse water quality impacts. These are detailed in a study by the San Francisco Estuary Institute. In the course of the restoration effort, the potential impacts are identified, mitigated where possible, and addressed through an adaptive management approach.


Niles Canyon Rapids

(The following information pertains to the Lower Alameda Creek Watershed within the jurisdiction of Alameda County Flood Control and Water Conservation District – from the mouth of Niles Canyon to San Francisco Bay.)

Seven creeks and flood control channels drain to the Alameda Creek Flood Control (ACFC) Channel in western Alameda County, forming significant subwatersheds within the Lower Alameda Creek Watershed, as described below. The north and south forks of Dry Creek drain the hills north of Niles Canyon; Crandall Creek drains the flatlands south of Alameda Creek; The District’s Zone 5, Line J2 drains the flatlands north of Alameda Creek; and Ardenwood Creek, within the Crandall Creek subwatershed, drains the floodplain between Crandall Creek and the managed ponds and wetlands, or “baylands,” of San Francisco Bay.

Lower Alameda Creek Subwatershed

Lower Alameda Creek is a 11 square-mile subwatershed comprised of the portion of Alameda Creek located in western Alameda County that begins near the mouth of Niles Canyon. From this point, Alameda Creek flows through the 12-mile-long Alameda County Flood Control Channel constructed by the Army Corps of Engineers in the 1970s. The channel passes through Union City and Fremont across the creek’s historic flood plain, then flows north of Coyote Hills Regional Park before reaching San Francisco Bay. With the construction of the flood control channel, Alameda Creek was diverted south of its historic route. Although the historic channel was left intact to form Old Alameda Creek, the western portion of the Alameda Creek Watershed bisected into north and south – old and new. For more information on the Old Alameda Creek Watershed, click here.

Dry Creek Subwatershed

Dry Creek is a 9.9-square-mile subwatershed that drains Walpert Ridge in the East Bay hills north of Niles Canyon. The north and south forks of Dry Creek meet near the terminus of Tamarack Drive in Union City. Both forks of Dry Creek run through Garin and Dry Creek Pioneer Regional parks, and through most of the subwatershed Dry Creek remains in its natural condition before its confluence with the ACFC Channel.

Crandall Creek Subwatershed

Crandall Creek is a 6.5-square-mile subwatershed comprised of Crandall Creek and Ardenwood Creek that once drained the floodwaters across the floodplain south of the historic Alameda Creek channel. Historically, Ardenwood Creek joined Crandall Creek just north of Coyote Hills, draining a riparian corridor thick with willows. From the point its confluence with Ardenwood Creek, Crandall Creek made a straight shot across the flatlands to the extensive tidal marsh that rimmed the south bay. Its former outflow to the bay is now the outflow of the ACFC Channel.One of the area’s largest and most productive historic farms, the Patterson farm, was located along Ardenwood Creek in what is now Fremont, taking advantage of the fertile soils in the alluvial fan of historic Alameda Creek. The Patterson family house and farm are now preserved as part of Ardenwood Regional Preserve. Commercial farming continues today at both Ardenwood and adjacent properties.Today Crandall Creek and Ardenwood Creek drain urban runoff through a series of culverts and engineered channels that flow into the Demonstration Urban Stormwater Treatment (DUST) Marsh, an artificial wetland designed to treat urban runoff, before eventually leading to San Francisco Bay. Its former outflow to the bay is now the outflow of the ACFC Channel.

Zone 5, Lines J2 & J3 Subwatershed

Zone 5, Lines J2 and J3 drains a 1.9-square-mile subwatershed in a residential area of Union City near the managed ponds and wetlands of south San Francisco Bay. A series of culverts drain to an engineered channel that joins the ACFC Channel.The shallow waters of south San Francisco Bay provided excellent conditions for the extensive tidal flats and tidal marshes that rimmed the shoreline. These same conditions made the south bay an excellent place for salt farming. Small scale salt production was a traditional activity of the Ohlone Native Americans, the Spanish, and early American settlers. From the mid-1800s through the late 1900s, salt production expanded to include large industrial ponds that transformed the south bay tidal flats and tidal marshes. In 2003, most of the salt ponds were purchased for restoration and are now part of the South Bay Salt Pond Restoration Project managed by the California Coastal Conservancy. Due to natural subsidence and that induced by salt production, many of these ponds will remain behind levees as either restored areas, managed tidal marshes, or managed ponds, all of which provide valuable habitat.
Recreational Opportunities
Tule Ponds

(The following information pertains to the Lower Alameda Creek Watershed within the jurisdiction of Alameda County Flood Control and Water Conservation District – from the mouth of Niles Canyon to San Francisco Bay.)

From Niles Canyon to the bay, there are two city parks, four regional parks, and a 12-mile-long regional trail within the Lower Alameda Creek Watershed. The parks provide water-oriented recreation, hiking, bicycling, and nature study and preserve the rich agricultural traditions in the former Alameda Creek floodplain. After flowing through parkland and urban developments, the Alameda Creek Flood Control (ACFC) Channel enters the bay through the Don Edwards San Francisco Bay National Wildlife Refuge.


The Alameda Creek Regional Trail extends 12 miles along the levee of the Alameda Creek Flood Control (ACFC) Channel from the mouth of Niles Canyon in Fremont to San Francisco Bay. The trail connects with Quarry Lakes Regional Recreation Area, Coyote Hills Regional Park, and the Don Edwards San Francisco Bay National Wildlife Refuge. Used most by cyclists, the entire trail along the south side levee is paved, including a loop that circles Coyote Hills.

Parks and Recreation

Quarry Lakes Regional Recreation Area

During the mid-19th century, the gravel deposits of Alameda Creek were mined in the area that is now Quarry Lakes Regional Recreation Area. Among other projects, the gravel was used in the construction of the transcontinental railroad. The leftover pits were later reclaimed by the Alameda County Water District for groundwater recharge. Today the Quarry Lakes cover 350 acres of the 471-acre recreation area, which is managed by the East Bay Regional Parks District (EBRPD). Boating, swimming, and fishing are popular activities. The recreation area is located on Quarry Lakes Boulevard in Fremont.

Niles Community Park

Operated by the city of Fremont, Niles Community Park contains three ponds in former gravel quarry pits adjacent to Quarry Lakes Regional Recreation Area. Located at 472 School Street, the park allows fishing and picnicking. The area in and around Shinn Pond is used as an off-leash dog park.

Garin and Dry Creek Pioneer Regional Parks

Managed by the EBRPD, Garin and Dry Creek Pioneer Regional parks share a contiguous border, together forming a 4,763-acre area in the hills behind California State University East Bay. The north fork of Dry Creek runs through Garin Regional Park and the south fork runs through Dry Creek Pioneer. Within the two parks, there are 20 miles of unpaved paths and two ponds. Jordan and Newt ponds were created by damming the north fork of Dry Creek. Today anglers fish the ponds for bass, bluegill, sunfish, and stocked catfish. Garin Regional Park sits on the former site of Garin Ranch, owned by Andrew Garin, who maintained large tracts of apple orchards. The ranch was sold to the EBRPD in 1966, but some of the antique apple varieties are still farmed today and celebrated at the annual Garin Apple Festival. A visitor center within Garin Park highlights the rich history of the area. Dry Creek Pioneer Regional Park sits on the former site of Dry Creek Ranch, which was owned by three sisters, Mildred, Edith, and Jeanette Meyers. During the 1950s and 1960s, the philanthropic Meyers sisters hosted fundraising events at the ranch. They eventually donated the 1,200-acre property to EBRPD in 1979 to prevent a freeway from bisecting it. The family cottage and Dry Creek Garden are preserved there today.

Ardenwood Historic Farm

The Ardenwood Historic Farm occupies the site of the Patterson family home and their successful farm from the 1850s. Historic Ardenwood Creek flowed through the farm, draining Alameda Creek floodwaters that, for thousands of years, deposited fertile farming soils in the area. Since 1985, the EBPRD and the city of Fremont have managed the site as a functioning turn-of-the-century farm and restored Victorian mansion. A docent program allows visitors to tour the mansion or participate in seasonal farming activities. The farm also supports the largest overwintering population of monarch butterflies in the Bay Area. A eucalyptus stand, along with EBRPD-maintained milkweed, keeps the monarchs here most years from December through February.

Coyote Hills Regional Park

Standing on San Francisco Bay levees looking east, the Coyote Hills appear as an island rising out of the flat Alameda Creek floodplain. West of the hills are the baylands, a series of managed ponds that are part of the Don Edwards San Francisco Bay National Wildlife Refuge. To the east are freshwater wetlands filled with water from Crandall and Ardenwood engineered creek channels. The EBRPD’s 978-acre Coyote Hills Regional Park was dedicated for public use in 1967. Today it is a popular place for hiking, bicycling, and bird watching. The park boasts a 2,000-year-old Tuibun Ohlone village and shellmound sites. The village contains an Ohlone-style family house, sweat house, and shade shelter that are open for guided tours with reservations. The park can reached via Patterson Ranch Road in Fremont.

Don Edwards San Francisco Bay National Wildlife Refuge

The ACFC Channel feeds into the northern extent of 30,000-acre Don Edwards San Francisco Bay National Wildlife Refuge. The baylands within the refuge consist primarily of tidal marsh, managed ponds, and mud flats. A smaller portion of the refuge includes seasonal wetlands and uplands. The refuge is home to 227 bird species and supports 45,000-75,000 wintering waterfowl each year. The refuge is also one of several entities partnering in the South Bay Salt Pond Restoration Project.

Eden Landing Ecological Reserve

The north levee of the ACFC Channel borders the 5,050-acre Eden Landing State Ecological Reserve. The reserve is undergoing restoration as Phase I of the South Bay Salt Pond Restoration Project. The public access opportunities and restoration effort at Eden Landing are described in depth here.

Restoration Efforts

Alameda Creek Fisheries
Multiple restoration projects are located within the Lower Alameda Creek Watershed that demonstrate both upstream creek restoration and downstream estuarine restoration.

Alameda Creek Fish Habitat Restoration

The restoration of ocean-run steelhead trout began in 1999 as a collaborative effort between the Alameda County Flood Control and Water Conservation District and several other agencies. It has been an extensive, ongoing project involving the removal of three dams and the construction of fish passage structures such as fish ladders. Stream flows will be improved for cold water fish, and habitat along the flood channel will be restored. With the completion of these projects, anadromous fish will be able to access up to 20 miles of spawning and rearing habitat in Alameda Creek and its tributaries.

South Bay Salt Pond Restoration Project

The 15,100 acres of industrial salt ponds in south San Francisco Bay will be restored through the South Bay Salt Pond Restoration Project, the largest tidal wetland restoration project east of the Mississippi River. The baylands at the outflow of ACFC Channel are included within this area. Their restoration will create a diverse habitat of tidal marsh and managed ponds for fish, waterfowl, and other wildlife. Phase I of the project restored Eden Landing at the mouth of Old Alameda Creek, just north of the ACFC Channel. As part of Phase II, levees will be modified near the lower reach of Alameda Creek to help create new tideland areas. Bay tides flowing in and out of the lower segment of Alameda Creek will scour sediment that might otherwise require dredging. The restoration of tidal marsh habitat is crucial to the survival of salmonids and marsh-dependent fish. Consequently, groups like the Alameda Creek Alliance are working to ensure that the salt pond restoration compliments the restoration of steelhead in Alameda Creek.

South Decoto Green Streets Project

This project covered eight full blocks in the neighborhood between 12th and 15th Streets and F and H Streets. It addressed storm drainage concerns and beautified the area by replacing old, flood-prone infrastructure with raingardens, permeable pavers and planted curb extensions. The project utilized low-impact best management practices to promote infiltration, provide temporary detention, and treat stormwater draining to Alameda Creek and its habitat. It transformed the streetscape with tree-lined, pedestrian-friendly space for community members and protects Alameda Creek from water pollution and high peak flows.