Located in Fremont, the 25.1-square-mile Laguna Creek Watershed drains the foothills of the Diablo Range south of Niles Canyon and includes the 2,500-foot Mission Peak within the Mission Peak Regional Preserve to the southeast. Morrison, Vargas, Mission, Washington, Sabercat, Canada del Aliso, and Agua Caliente creeks drain the expanse of foothills, flow across the flatlands through underground culverts and engineered channels to meet Laguna Creek and finally Mud Slough on the way to San Francisco Bay. Along the shoreline of Mud Slough is the ghost town of Drawbridge and a harbor seal haul out.

Laguna Creek Watershed

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Flora and Fauna

The Laguna Creek Watershed drains two very different ecosystems: the Diablo Range at higher elevations and tidal marshes and tidal flats near the bay. Common trees throughout the Diablo Range include coast live oak, valley oak, blue oak, Mexican elderberry, Pacific madrone, and gray pine. Riparian species include white alder, California sycamore, and willow. Cattle dot the grasslands all the way to the top of Mission Peak and down to the edges of suburban development. In the spring, wildflowers are abundant, including California poppy, monkey flower, and several species of lupines. The East Bay Regional Park District publishes a wild plant checklist for all plants found within Mission Peak Regional Preserve. Many small mammals live here and a few carnivores, such as coyotes. Also present is the Diablo Range garter snake, which is very similar to the California garter snake but named for its local habitat.

Mud Slough meanders across the marsh plain between salt ponds and tidal marsh that were recently restored as part of the South Bay Salt Pond Restoration Project. Part of the Don Edwards San Francisco Bay Wildlife Refuge, this area is home to hundreds of bird species and is a stopover for 45,000-75,000 wintering waterfowl each year. Mud Slough branches off of the deep and wide Coyote Creek channel into an area with limited public access to protect wildlife. In this relatively undisturbed location, harbor seals haul out onto the marshes where they give birth and raise their pups.

Geology and Hydrology

The flatlands within the northern Laguna Creek Watershed lie on the outer expanse of alluvial soils deposited over thousands of years by the floodwaters of Alameda Creek. These silty and sandy soils made for productive farming throughout the 1900s. The remainder of the watershed drains Miocene epoch sedimentary rock along the Diablo Ridge, which was formed by uplift along the east side of the strike-slip Hayward Fault. Stivers Lagoon, later modified into Lake Elizabeth, formed where the fault created a sag pond—a scarp and depression in which water accumulates. 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. For the last several thousand years, creeks have flowed from the Diablo Ridge into Laguna Creek and through Mud Slough across miles of marsh plain thick with vegetation and branching waterways. Click here to read about the formation of the south San Francisco Bay tidal marshes as its described in the Geology and Hydrology section of the Mowry Slough watershed page.

Major Issues

Within the Laguna Creek Watershed, water contamination levels are consistent with urban areas in the region. Mercury, PCBs, and PBDEs are the greatest concerns, though dioxins, PAHS, and selenium are also problematic. While overwhelming evidence demonstrates the potential of tidal marshes to improve water quality, large-scale restoration activities in the South Bay may have their own water quality impacts. The San Francisco Estuary Institute studied these impacts during the planning process for the South Bay Salt Pond Restoration Project. Its report addressed the potential for accelerated erosion of buried sediment as well as increased net production of methyl mercury and its subsequent accumulation in the food web. Measures to reduce these impacts are being taken as the project proceeds. Salt ponds along the southern edge of Mud Slough were restored in the first phase, and ponds to the north are slated for restoration in the second phase. Most important, the project employs a phased adaptive management approach, enabling scientists to monitor and identify issues that arise, then modify the project’s approach to address them.

Major Creeks & Waterbodies

Located in the city of Fremont, the Laguna Creek Watershed comprises nine major creeks that are fed by runoff from both urban and undeveloped areas during winter and spring storms and by natural springs in the foothills of the Diablo Range. The watershed also includes Lake Elizabeth, a manmade lake created from a natural lagoon, and Mud Slough, which, along with Coyote Creek, drains the watershed across the marsh plain to San Francisco Bay.

Mission Creek

Beginning on the east side of the 2,517-foot Mission Peak in Fremont, Mission Creek flows northwest draining the east side of the Mission Hills until it reaches the first valley though which it can cross to the urban flatlands. It parallels Mill Creek Road to Mission Boulevard just south of I-680. From there, culverts carry it around the freeway and return it to its natural drainage to be joined by Vargas Creek. Continuing northwest it enters an engineered channel at Driscoll Road, flows through Gomes Park, then on to Lake Elizabeth in Central Park, where it is joined by Morrison Creek.

Vargas Creek

Vargas Creek drains the foothills surrounding the Mission Valley neighborhood of Fremont near I-680. The creek is in its natural channel through the valley and foothills, then runs through culverts along the I-680 corridor to Mission Creek.

Morrison Creek

Morrison Creek drains the hills south of Niles Canyon, flowing westerly until it reaches the base of the hills. There, it turns south and flows through an engineered channel to Lake Elizabeth, where it joins Mission Creek.

Lake Elizabeth and Stivers Lagoon

Located on the Hayward Fault off Paseo Padre Parkway, Lake Elizabeth is the focal point of Fremont’s 450-acre Central Park. The manmade lake was created by expanding Stivers Lagoon, a natural, 200-acre, deep water lake and fresh water marsh. Through the 1800s, the lagoon was altered by the construction of levees and tule harvesting. In the 1950s, the Stivers family sold the property to the Alameda County Flood Control and Water Conservation District, which in turn leased it to the City of Fremont as a nature preserve. Today, Central Park includes a 40-acre nature area at Stivers Lagoon, the 88-acre Lake Elizabeth, a swimming area, four playgrounds, a sports complex, soccer fields, tennis courts, and a picnic area.

Laguna Creek

Laguna Creek was named for the natural lake (“laguna” in Spanish) from which it flowed. Starting at Lake Elizabeth, it now flows southeast through an engineered channel that leads to and then parallels Fremont Boulevard. It is joined by Sabercat Creek between Haven Avenue and Ronald Court. At the intersection with Fremont and Old Warm Springs boulevards, the channel (*Line E) cuts southwest and leads to Mud Slough, winding through salt ponds and industrial development along the way.

Sabercat Creek

In the foothills northwest of Mission Peak are several small forks of Sabercat Creek that drain the Mission neighborhood of Fremont. Almost immediately upon exiting the foothills, the forks flow into underground culverts that lead to Sabercat Creek. The creek stays in its natural state crossing Pine Street near Ibero Way, then enters a greenbelt with a creekside trail until it crosses under I-680. From there, it flows through an engineered channel and joins Laguna Creek.

Washington Creek

Washington Creek begins in the foothills and flows west, parallel to Washington Boulevard, intermittently flowing below ground and then in its natural channel. After crossing I-680, the creek follows its natural course to Osgood Road, where it is diverted through culverts to join Sabercat Creek.

Canada del Aliso

The hills due north of Mission Peak are drained by two forks of Canada del Aliso. The creeks run nearly parallel to Mission Boulevard, where they are diverted to underground culverts that collect runoff and carry the flow under I-680 to two engineered channels. The channels empty into Laguna Creek at Old Warm Springs Road a quarter mile south near the railroad tracks.

Agua Caliente Creek

Agua Caliente Creek drains Mission Peak, flowing west through Mission Peak Regional Preserve and the suburban neighborhood that abuts it. Between Paseo Padre Parkway and Tumbleweed Common, eroding creek banks were restored by the Alameda County Flood Control and Water Conservation District. Agua Caliente Creek is joined by several unnamed creeks before flowing into underground culverts through an industrial area across I-680. It then resurfaces and flows southwest to an engineered channel (*Line F) that joins Laguna Creek at the salt ponds.

Mud Slough

Mud Slough separates from the larger Coyote Creek, then meanders north through the ghost town of Drawbridge. Created in 1876, the town was the home of the operator of the Southern Pacific Railroad drawbridges. What remains today is a gathering of decaying residences on the marsh plain near the drawbridge that crosses Mud Slough. Surrounded by salt ponds, the slough curves north where it meets Laguna Creek (*Line E) at the line of development. Harbor seals haul out along the banks as it meanders across the marsh plain. The salt ponds north and south of the slough are designated for restoration as part of the South Bay Salt Pond Restoration Project. The restoration of the ponds between Mud Slough and Coyote Creek was completed in 2009.

Coyote Creek

In aerial photos of San Francisco Bay, the South Bay looks as though it has octopus-like tentacles extending from the edges. Those are natural sloughs and creeks that wind through the marsh plain and Coyote Creek is the largest of them with several sloughs branching off from it, including Mud Slough. The creek is large enough to send salt water into tidal marshes far inland from the tidal mud flats near the shoreline and deep enough for harbor seals to travel and feed.

* A naming system used by the Alameda County Flood Control and Water Conservation District

Recreational Opportunities


Mission Peak Trails

East of Fremont, the Mission Peak Regional Preserve provides access to Mission Peak, part of the Diablo Range that includes Mount Allison and Monument Peak. There are two main trailheads for hiking to the 2,517-foot summit. The first is accessible from the Ohlone College parking lot and takes a more gradual ascent. It is part of the Bay Area Ridge Trail, a planned 550-mile multi-use trail (currently over 330 miles are complete) along the hill and mountain ridgelines ringing the San Francisco Bay Area. The second starts in a small lot at the east end of Stanford Avenue in Fremont and climbs steeply to the summit. From either route, the top of Mission Peak offers views of the entire Bay Area and beyond: Mount Hamilton to the south, the Santa Cruz Mountains to the west, Mt. Tamalpais to the north, and Mt. Diablo and the Sierra Nevada to the northeast.

San Francisco Bay Trail

The San Francisco Bay Trail (Bay Trail) is a planned shoreline trail encircling the entire bay. In the area southeast of Mud Slough, a small, completed segment of the trail provides views of the marsh plain and beyond. The trail runs on top of the inboard levee along an estuary fed by both Mud Slough and Coyote Creek into the Agua Fria Creek Watershed west of I-880.

Parks and Recreation

Mission Peak Regional Preserve

The 3,000-acre Mission Peak Regional Preserve is located east of Fremont in the Diablo Range and includes Mission and Monument Peaks. Although the two main trails leading to the taller Mission Peak are the most popular, other trails run throughout the park. The East Bay Regional Park District provides trail maps at trailheads and online. Also within the preserve is the Eagle Spring Backpack Camp (reservations required) and a hang-gliding and paragliding launch site. Gliders are often spotted riding wind currents alongside hawks and vultures.

Gomes Park

A city park located at 827 Lemos Lane in Fremont, Gomes Park offers grassy areas for recreation and a play structure. Mission Creek meanders through the park in a sinuous tree-lined channel–a far cry from its appearance before the park was created: a straight ditch dug to keep the shifting creek from flooding farms.

Don Edwards San Francisco Bay National Wildlife Refuge

Laguna Creek, Mud Slough, and Coyote Creek drain through the 30,000-acre Don Edwards San Francisco Bay National Wildlife Refuge. This vast wetland preserve extends from the Coyote Hills south, past Dumbarton Point and through the South Bay. The refuge is home to 227 bird species and supports 45,000-75,000 wintering waterfowl each year. Miles of trails run along the crests of the old dikes located north and south of the Mowry Slough watershed.

Restoration Efforts

The Laguna Creek Watershed is the site of many projects that exemplify both upstream creek restoration and downstream estuarine restoration.

Agua Caliente Creek Restoration

Beginning in 2009, the Alameda Flood Control and Water Conservation District (the District) embarked on a bank stabilization project in Agua Caliente Creek where it crosses Tumbleweed Common. The project realigned and widened the creek bed to stabilize banks, combatting years of heavy erosion. Native plants, grasses, and trees were added to existing native vegetation to support wildlife, such as the endangered California red-legged frog.

Sabercat Creek and Trail Restoration

Sabercat Creek is one of the last natural riparian areas in Fremont and an important archeological site. But erosion is so severe that banks are crumbling into the creek, sending increasing amounts of sediment downstream and clogging up waterways. The city of Fremont won a grant from the California Natural Resources Agency’s California River Parkway Program to restore a section of the creek from above Paseo Padre Parkway to Via Orinda. Working with the District, project managers added rock structures to slow storm water and reinforced creek banks with natural materials. A bioswale with native plants improves drainage and water quality. The project also included restoring the trail, creating a new picnic area, replacing non-native with native plants, and providing several new pedestrian paths to enhance recreation and educational opportunities.

Another restoration project along Sabercat Creek is funded by the Bay Area Rapid Transit District and conducted in partnership with the city of Fremont. This project includes removing non-native and invasive species and replanting within the riparian corridor to diversify vegetation and increase habitat value.

Alviso Salt Ponds

The South Bay Salt Pond Restoration Project covers three major areas: Eden Landing, Ravenswood, and Alviso. Phase I of the project restored salt ponds in the Alviso area between Mud Slough and Coyote Creek (also known as Pond A6). Project managers, scientists, and engineers created 330 acres of tidal salt marsh and tidal channel habitat and enhanced 240 acres of shallow ponds, adding 50 nesting islands for migrating shorebirds. New marsh and shallow water habitats for pelicans, cormorants, and ducks were created by reconnecting an additional 1,400 acres of ponds to the bay.

Get Involved

There are several organizations that fund or provide free watershed education programs and volunteer opportunities in the Laguna Creek Watershed. The websites below may include additional links to other organizations and resources.