Monday, January 7, 2019

Miller Creek Watershed

Miller Creek Watershed

History and Habitat

Human Settlement

The Miller Creek Watershed is the northernmost part of the north San Rafael land grant (San Pedro, Santa Margarita y Las Gallinas). The land was originally granted to Timothy Murphy who incurred the gratitude of Governor Alvarado in 1837 by helping him defend against a coup attempt.

James Miller later bought 680 acres of the Las Gallinas portion of the rancho and operated it as a beef ranch and then as a dairy farm. Miller assisted the Sisters of Charity running the St. Vincent School, established 1855 as a girls’ seminary. The school eventually closed due to a lack of students and later became a school for orphaned boys.

The valley portions of the watershed were developed for urban housing beginning in 1955. The most recent development, Miller Creek Estates, was constructed in the 1980s and early 90s.

Changes to Watershed Processes

Miller Creek is an atypical east Marin creek in that it has a relatively intact riparian area with very high widths and depths relative to its drainage area. In many locations throughout Miller Creek the banks are 20 to 25 feet high and its width is often over 100 feet (Philip Williams and Associates, Ltd. 19811).

The creek has gone through two recent cycles of incision, or arroyo formation since the arrival of Europeans. Mid 19th century riparian vegetation clearing and grazing practices initiated the first cycle of channel downcutting. A second cycle started after the 1940s as evidenced by the disparate channel bed elevations upstream and downstream of the Grady Bridge and concrete apron installed in 1941; the channel downstream is 10 feet lower than the bed immediately upstream. Increased runoff and changes to drainage patterns from valley housing developments may have contributed to this rapid lowering of the channel bed. This incision occurred at a rate of approximately 1 foot per 10 years (PWA 1981). Recent channel assessments indicate that the rate of mainstem incision has slowed or stopped due to either the channel reaching a stable bed condition, increased sediment supply from tributary incision, or the installation of grade stabilization structures (Yin and Pope-Daum 2004 2).

With channel incision comes bank instability and widening. Vertical banks are undercut by moderate flows, with bank slumping and retreat occurring until there is sufficient width to accommodate flood flows and develop inset floodplains and terraces.

In the lower reaches of the valley the channel is wide with well developed and vegetated inset floodplains and an inner terrace. Bank instability at the outside bends of the channel meanders occurs throughout the valley as the channel continues to widen.

The Miller Creek Estates and Upper Miller Creek channel reaches were graded into a trapezoidal channel during housing development construction in the 1970s and 1980s. These reaches have a 100 foot setback along the channels. A post- project evaluation of this stretch of Miller Creek by Yin and Pope-Daum (2004) indicates that riparian vegetation has established in these reaches and the creek has developed a low-flow channel and discontinuous floodplains. Bank erosion is concentrated at the outside of meander bends. The channel complexity and habitat features are not as well developed as in the non-graded reaches downstream; however, the Miller Creek Estate reach has better habitat conditions than have been observed in the upstream reaches that are characterized by vertical banks, a wide homogenous channel bottom, and little mature riparian vegetation.

Tributary channels have undergone extensive downcutting and gully formation in response to the main channel incision. Headcut retreat is occurring in many steep, first order channels. Large volumes of sediment are delivered to the mainstem from tributary erosion and fine sediment aggradation reduces pool depths and degrades spawning gravels. The sediment produced by the upper watershed is deposited in the lower reaches of the system.

Downstream of the NWPRR Bridge the channel was rerouted and channelized in the 1920s. The creek was routed to the south, extended, and placed into a narrow, leveed channel with two 90 degree bends before reaching San Pablo Bay. A stretch of tidal wetlands are present along the bay front. There is local interest in realigning the creek east of the NWPRR Bridge to provide a more natural, direct connection to San Pablo Bay (Marin Conservation League 1997 3; St. Vincent’s/Silveira Advisory Task Force 2000 4).

Bank erosion in mainstem Miller Creek is widespread, as the channel is deeply incised in many places and in a widening phase. This erosion typically occurs on the outside of meander bends and is characterized by vertical banks with little to no riparian vegetation (H.T. Harvey and Associates 1992 5, PCI 2004 6). Often this bank erosion jeopardizes private property and structures.

Historic grazing practices and recent mainstem channel incision has caused destabilization of tributary channels. In the uplands, first and second order channels are undergoing headcutting and gully development, delivering fine sediment to Miller Creek during storm events. Visual assessments of instream sediment deposits indicate that there may be a higher than normal amount of fine sediment in the system, which leads to degraded instream habitat for fish and other species.
Habitat Types

The Miller Creek watershed is a mosaic of open ridge lands and grazing lands in the upper watershed, residential and limited commercial development along the narrow valley floor, and lower baylands. It is a relatively urbanized watershed but still supports a small population of steelhead, an important resource for the regional fishery. Some stretches of the creek still support somewhat healthy riparian plant communities. The lower marsh habitats represent some of the largest remaining tidally-influenced habitats in the bay region and support abundant waterfowl populations (Goals Project 1999 7)The Las Gallinas Valley Sanitary District reclamation ponds adjacent to the marshes are one of the premier birding spots in Marin County. The Marin Countywide Plan (OS2.4) identifies Miller Creek as an important area for habitat connectivity providing continuous natural area through Miller Creek and Marinwood to the Bay.

The watershed is composed primarily of annual grasslands interspersed with oak-bay woodland and oak savanna in the upper watershed with patches of chaparral. The upper watershed is largely Marin County Open Space ridge lands and grazing lands. Historically, the upper watershed was heavily grazed and the riparian habitat is somewhat degraded. The most well-developed riparian plant communities occur west of Highway 101 near Miller Creek Middle School upstream towards Mt. Shasta Drive. Urban areas dominate the middle reaches of the watershed and the bulk of the population is concentrated along the narrow valley floor.

The lower reaches of the watershed east of Highway 101 support saltwater marsh and brackish-water marsh, both subject to tidal action. Freshwater seasonal wetlands occur in areas that were once historical baylands. These areas were diked off to provide agricultural land and now support oat hay production. The reclamation ponds created by Las Gallinas Valley Sanitary District adjacent to tidal marshes in the lower watershed provide critical habitat for a number of bird species. This area boasts over 200 bird species and includes such sightings as golden eagle, ferruginous hawk, and rails. River otters are also known to frequent the area.

The St. Vincent’s School for Boys and Silveira Ranch are treasured parts of the Marin County landscape and provide critical habitat within the lower Miller Creek watershed. The site supports “oak woodlands, valley oak savanna, tidal and seasonal wetlands, historic diked tidelands, seeps and swales, the Miller Creek riparian corridor, and grassland” habitats (St. Vincent’s/Silveira Advisory Task Force 2000). Pacheco Ridge at the upper elevations of site supports intact native oak woodlands, an important habitat resource and community separator. The central location of the site provides habitat connectivity between “the Gallinas Creek watershed to the south, San Pablo Bay to the east, and Hamilton tidal marshes to the north” (St. Vincent’s/Silveira Advisory Task Force 2000).

Fish and Wildlife

The watershed supports a number of special-status plants and animals. Of particular interest are the occurrences of wetland-adapted species along the lower baylands. Noteworthy species include San Pablo song sparrow, California black rail, saltmarsh harvest mouse, and California clapper rail.

The Miller Creek watershed is also known to support 7 extant fish species (6 native and 1 introduced) and one extinct native species (Leidy 2007 8). Native species include California roach, steelhead, threepine stickleback, staghorn sculpin, prickly sculpin, and riffle sculpin. Common carp have also been introduced. Historically, the watershed supported native Sacramento sucker.

Steelhead have been observed within the Miller Creek watershed as recently as 2006.

There are no reported occurrences of federally-listed as threatened and California Species of Special Concern California red-legged frog within the watershed (CDFG 2008 9).

Heron and egret nesting colonies have been monitored by Audubon Canyon Ranch since the early 1990s (Kelly, et al., 2006). There are active nest colonies on shrub-covered islands at Las Gallinas Valley Sanitary District plant at the east end of Smith Ranch Road. Black-crowned night-heron, snowy egret, and great egret have been observed nesting on the islands. Nests are in low-growing (1 meter) shrubs (Condenso, personal communication, May 15, 2008; Kelly, et al., 2006 10).

In addition, the Las Gallinas Valley Sanitary District reclamation ponds support over 200 bird species.

Human Habitation and Land Use

Current land use

In 1960, Marinwood, Miller Creek, and associated communities organized a community services district responsible for fire protection, parks and recreation, street lighting and open space. The Marinwood Community Services District now owns 812 acres of open space in the watershed including part of the ridge between the Miller Creek watershed and Novato. The developed area of the watershed fills the valley, with large portions of the ridges in Marin County Open Space District ownership and the balance held in private ranches. 13% of the watershed is incorporated areas.

The Marin County Open Space District, City of San Rafael, and Marinwood Community Services District also own substantive portions of the Miller Creek riparian area.

Marin County has identified the Marinwood Shopping Center as a potential site for community-based planning creating workforce housing within the City-Center corridor in mixed-use development. The Countywide Plan calls for 50-100 units in this area, as per the Marinwood Plaza Conceptual Master Plan.

1 Land & Water Management for Upper Miller Creek and Environs

2 Post project evaluation, Miller Creek, California: assessment of stream bed morphology, and recommendations for future study

3 Miller Creek Restoration Feasability Study Calfed Proposal 1997 category III

4 St. Vincent's/Silveira Advisory Task Force Recommendations

5 Channel Stabilization and Restoration Design for Two Sites on Miller Creek Marinwood CSD Reach, San Rafael, CA

6 Summary of channel assessment and design for Miller Creek Lassen-Shasta Reach (aka Darwin Reach)

7 Baylands Ecosystem Habitat Goals: A Report of Habitat Recommendations

8 Robert A. Leidy, Ecology, Assemblage Structure, Distribution & Status of Fishes in Streams Tributary to the San Francisco Estuary

9 California Department of Fish and Game (CDFG). 2008. California Natural Diversity Database. California Department of Fish and Game, Sacramento, CA.

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



Land Use


Large detailed versions of
these maps are available
in the Resources section.

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