San Rafael Creek Watershed

San Rafael Creek Watershed map

Watershed Overview


The San Rafael watershed comprises 11 square miles and is densely developed from its hills to filled wetlands.  The creek originates in the hills above Tamalpais Cemetery and flows through residential and industrialized areas before forming the San Rafael Canal in the vicinity of Highway 101.  The upper stream corridor consists of short stretches of open stream channel, underground culverts, and trapezoidal open channels.  The creek enters San Rafael Bay at Pickleweed Park.  San Rafael Creek and Canal, once important commercial waterways in Marin, are currently used as marinas for recreational watercraft.  Habitat for native species is provided by a small marsh at Pickleweed Park, and a handful of intact woodland, grassland, and lagoon areas occur in the northern edge of the watershed.


Watershed History

Human Settlement

Most of the San Rafael watershed was originally part of the Santa Margarita, Las Gallinas y San Pedro land grant given to Timothy Murphy in 1844.  The San Rafael watershed is at the southern end of the grant (Miller Creek and Gallinas Creek watersheds are located in the northern portion of the grant).  The area that is now downtown San Rafael was part of the Mission San Rafael Archangel established in 1814.  An area in the southern potion of the watershed, much of which has been filled, was originally designated as “swamplands”.

The land was originally used for grazing and agriculture by the Mission and Rancho.  It soon developed into a desirable location for vacation and second homes.  San Rafael was the original seat of government for Marin County, established in 1850 at the time California became a state.  By the mid-to-late 1800s, San Rafael was a flourishing city accessed by train and ferry from San Francisco.  The San Rafael Canal was important for early industry and as a recreation destination; in the early 1900s, the Canal was dredged near the Irwin Street bridge to create the San Rafael Baths, pools 35 feet wide and 200 feet long.  In 1928, the U. S. Army Corps of Engineers began widening and dredging the Canal for navigation.


Watershed Today

Changes to Watershed Processes

The streams of the San Rafael Creek watershed originate on the slopes of the San Rafael Hills and San Pedro Point.  They quickly reach the City of San Rafael and begin to exhibit the characteristics typical of highly urbanized creeks.  Many of them, especially Mahon Creek, Irwin Creek, Lincoln Creek, and Black Canyon, have been channelized and sections have been routed under the city in culverts.  A reach of Mahon Creek between B Street and Highway 101 was restored in 2001.  This reach is tidally influenced with wetlands bordering the channel downstream of Lindaro Street. The reach between B and Lindaro streets is straight and trapezoidal.

Dense urban development on former tidal wetlands has constricted San Rafael Creek and reduced the ability of the channel to flush sediment out and maintain channel capacity as part of the tidal cycle.

Habitat Types



The watershed is highly urbanized, with small outcroppings of annual grasslands and oak-bay woodland.  The upper slopes of the watershed adjacent to Mount Tamalpais Cemetery are Marin County Open Space District ridge lands.  In the upper watershed, where the channel is open and not restricted to underground culverts, the banks are typically dominated by non-native plants.  Developed urban uses often abut the creek bank.  The upper watershed is ephemeral to intermittent during higher flow years and currently does not support fish populations. Isolated wetlands along the bay provide the most important biological resources within the watershed.  

Near downtown San Rafael and extending downstream of Highway 101, the creek is tidally influenced and contained within a man-made channel (the San Rafael Canal).  During low tide, mudflats become exposed along the channel banks.  The canal enters the bay near Pickleweed Park.  A 4-acre tidal marsh at the park supports a small population of California clapper rail.  Marsh habitat along the bay is highly fragmented but still supports salt marsh harvest mouse, San Pablo song sparrow, and common yellowthroat—all salt marsh adapted species.  The open bay, intertidal areas and mudflats also provide habitat for migratory waterfowl, shorebirds, and wading birds.

Along the northern watershed boundary, upslope of Point San Pedro Road, Harry Barbier Park supports a number of intact communities including oak-bay and oak woodlands, grassy meadows, and coastal scrub.  The park provides habitat connectivity between the San Rafael and Gallinas Creek watersheds.  Sudden oak death (SOD) is prevalent in the park.  Originating in the Harry Barbier Park, a small bay drainage, Glen Creek, supports threespine stickleback, Pacific treefrog, and the occasional river otter (Personal communication, L. Lewis 2008).  The 140-acre Peacock Gap Golf and County Club property supports a number of small freshwater ponds and a larger 13-acre tidal lagoon (Hydroikos Ltd. 2000 1).  Areas of healthy, mature woodland habitats surround the club property.

Along the northern watershed boundary, there is a small bay drainage, Glen Creek, City of San Rafael owned Harry Barbier Park, and the privately owned Peacock Gap Golf Course and County Club.  Harry Barbier Park supports native woodland and grasslands and Peacock Gap Golf Course and County Club supports some native woodlands, several freshwater ponds, and a 13-acre tidal lagoon.  To the south of Pickleweed Park along the baylands, there is a small lagoon owned by the City of San Rafael with several small islands.

Just offshore of San Rafael are two small islands managed as part of the San Pablo Bay National Wildlife Refuge.  While they are not technically part of the watershed, they are ecologically connected:

“The Marin Islands sit off of San Rafael along the Marin County shoreline of San Francisco Bay.  The two small islands and surrounding tidelands, protected by the Marin Islands National Wildlife Refuge and State Ecological Reserve, support one of the largest egret and heron rookeries in northern California.  West Marin Island, the smaller of the two, provides nesting habitat for great egrets, snowy egrets, great blue herons, black-crowned night-herons, western gulls, and ravens.  Its neighbor, East Marin Island, was once used as a vacation retreat and has been overrun with invasive species including Scotch broom, fennel, and eucalyptus.  However, the larger island still provides valuable nesting material for the rookery next door.” (Save the Bay 2008 2).

Fish and Wildlife

The watershed supports a few special-status plants and animals, primarily in marsh habitat along the Bay.  Noteworthy species include California clapper rail, San Pablo song sparrow, salt marsh harvest mouse, and Marin western flax.  Tiburon buckwheat occurs at higher elevations in Black Canyon extending into Harry Barbier Park.



Historically, the watershed may have supported steelhead and other fish. Lewis (Personal communication, 2008) noted the presence of threespine stickleback in Glen Creek, a bay tributary to the north of San Rafael Canal.  Currently, the upper watershed is not known to support fish due to a lack of habitat and perennial water.  The lower tidal sloughs likely support estuarine fish; however, there are no reports documenting their occurrence.

There are no reported occurrences of California red-legged frog, federally-listed as threatened and California Species of Special Concern, within the watershed (CDFG 2008 3).  There are no reported occurrences of northwestern pond turtle, a California Species of Special Concern, within the watershed (CDFG 2008).  The watershed does support Pacific treefrog.

Heron and egret nesting colonies have been monitored by Audubon Canyon Ranch (Kelly, et al., 2006 4).  As discussed above in the Habitat section, the Marin Islands National Wildlife Refuge was established in 1992 to protect the large heronry on West Marin Island.  The colony has been in existence and actively monitored since the late 1970s.  It currently supports black-crowned high-heron, snowy egret, great egret, and great blue heron.  In recent years, approximate counts have shown 200 black-crowned night-heron, 100 snowy egret, 150 great egrets, and a handful of great blue herons have been documented using the site (see Kelly, et al., 2006).

In 2007, an estuary-wide breeding season survey for California clapper rails was conducted as part of the Invasive Spartina Project.  At the time of the survey, Pickleweed Park supported 2 to 4 clapper rails and a number of other bird species.

Human Habitation and Land Use

Land UseImperviousness

Land Use                                        Imperviousness

Approximately 80% of the San Rafael watershed is developed, with the City of San Rafael occupying almost 90% of the watershed (this includes developed and undeveloped portions of the City).  The largest open space areas are the southern portions of China Camp State Park and San Pedro Mountain.  The watershed including the Central San Rafael, Downtown, and East San Rafael planning areas.  A very small area in the upper watershed, the San Rafael Ridge, is county-owned open space, part of the Terra Linda-Sleepy Hollow Divide Open Space Preserve.

Development intensity ranges from hillside residential areas, generally divided into 2-acre lots, to downtown areas with as many as 62 units per acre.  The southeast industrial area is built on the historic swamplands discussed above. 

There are four unincorporated areas in the watershed: California Park, Upper Sun Valley, Bayside Acres and Country Club, and Point San Pedro.  California Park is located between San Quentin and Highway 580.  Upper Sun Valley is located on the west edge of San Rafael.  It is approximately evenly divided between residential, open space, and the Mount Tamalpais Cemetery.  Bayside Acres and Country Club are small pockets of unincorporated area along Point San Pedro Road.  Point San Pedro is zoned as mineral resource and is used for rock extraction.  The largest land user in the area is the Marin Sanitary Service, which operates the county waste collection, a recycling center, and a hazardous waste disposal program in collaboration with the City of San Rafael and the County of Marin.

Development within the City of San Rafael is anticipated to be mostly infill and redevelopment, because most of the available parcels have already developed.  San Rafael’s General Plan 2020 calls for 43% open space, but that is likely to occur largely in north San Rafael in the Gallinas and Miller Creek watersheds.  After the Point San Pedro Quarry ceases operation, the area is planned for mixed residential, commercial, recreational, and marina use.

1 Peacock Lagoon Water Quality Study


3 California Department of Fish and Game (CDFG). 2008. California Natural Diversity Database

4 Annotated Atlas and Implications for the Conservation of Heron and Egret Nesting Colonies in the San Francisco Bay Area