The watershed is highly urbanized and is developed from its hills to filled wetlands. It has small outcroppings of annual grasslands and oak-bay woodland. The upper stream corridor has short stretches of:
- Open stream channels
- Underground culverts
- Trapezoidal open channels
The upper slopes of the watershed adjacent to Mount Tamalpais Cemetery are Marin County Open Space District 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 has seasonal water flows, known as ephemeral to intermittent during higher flow years. It does not currently support fish populations. Isolated wetlands along the bay provide the most important biological resources within the watershed.
San Rafael Canal
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. Tiscornia Marsh at Pickleweed Park provides a habitat for native species. There are also intact woodland, grassland, and lagoon areas that can be found in the northern edge of the watershed.
A 4-acre tidal marsh at the park supports a small population of Ridgway's rail. Marsh habitat along the bay is highly fragmented but still supports salt marsh adapted species, including:
- Salt marsh harvest mouse
- San Pablo song sparrow
- Common yellowthroat
The open bay, intertidal areas and mudflats also provide habitat for migratory waterfowl, shorebirds, and wading birds.
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.
Harry Barbier Park
Along the northern watershed boundary, upslope of Point San Pedro Road, is Harry Barbier Park. It 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 called Glen Creek supports:
- Threespine stickleback
- Pacific treefrog
- River otter
Peacock Gap Golf and County Club
The 140-acre Peacock Gap Golf and County Club property supports a number of small freshwater ponds and a larger 13-acre tidal lagoon.
Areas of healthy, mature woodland habitats surround the club property.
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
The watershed supports a few special-status plants and animals, primarily in marsh habitat along the Bay. Noteworthy species include Ridgway's 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. The presence of threespine stickleback has been noted in Glen Creek, a 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 year-round or perennial water. The lower tidal sloughs likely support estuarine fish. There are no reports, however, documenting their occurrence.
There are no reported occurrences of California red-legged frog or northwestern pond turtle within the watershed. (The red-legged frog is federally-listed as threatened and both are California Species of Special Concern.) The watershed does support Pacific treefrog.
Heron and egret nesting colonies have been monitored by Audubon Canyon Ranch. 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
A handful of great blue herons have been documented.
In 2007, an estuary-wide breeding season survey for Ridgway's rails, (then known as California clapper rails) was conducted as part of the Invasive Spartina Project. At the time of the survey, Pickleweed Park supported 2 to 4 rails and a number of other bird species.
Approximately 80% of the San Rafael watershed is developed. The City of San Rafael occupies 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 includes the Central San Rafael, Downtown, and East San Rafael planning areas. A very small area in the upper watershed called the San Rafael Ridge is county-owned open space. This is 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 historic swamplands.
There are four unincorporated areas in the watershed:
- California Park
- Upper Sun Valley
- Bayside Acres and Country Club
- 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. They operate 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.
Changes to the watershed
The streams of the San Rafael Creek watershed begin on the slopes of the San Rafael Hills and Point San Pedro. They quickly reach the City of San Rafael and begin to exhibit the characteristics typical of highly urbanized creeks.
Many of them have been channelized and sections have been routed under the city in culverts, especially:
- Mahon Creek
- Irwin Creek
- Lincoln Creek
- Black Canyon
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. This has reduced the ability of the channel to flush sediment out and maintain channel capacity as part of the tidal cycle.
- Peacock Lagoon Water Quality Study
- Save San Francisco Bay website
- California Department of Fish and Game (CDFG). 2008. California Natural Diversity Database
- Annotated Atlas and Implications for the Conservation of Heron and Egret Nesting Colonies in the San Francisco Bay Area