Novato Creek Watershed

Richardson Bay

Draft Watershed Workplan


The purpose of the Novato Watershed Program is to identify opportunities to integrate flood protection goals with creek and wetland restoration elements.  This process includes evaluating alternatives that would reduce flood protection maintenance costs and impacts and be resilient to sea level rise.  This first phase of work would produce a unified hydrology and hydraulics model to evaluate alternatives and a Geographic Information Systems based database to identify restoration opportunities.  Once the multi-benefit alternatives are identified, it is anticipated a revenue measure would be proposed to fund implementation.  This work would also support efforts to secure grant funds.


In 2006, the Marin County Flood Control District completed the final phase of a 15 year, multi-phase flood control project that provides protection from the 50-year storm event along the lower reaches of Arroyo Avichi, Warner, and Novato Creeks.  The floods of 2006 revealed that additional work along lower Novato Creek could reduce potential flooding impacts to Nave Gardens and downtown Novato.  During the 2006 floods, downtown Novato would have experienced flooding had the levee at Deer Island basin not been breached. Flood protection in downtown Novato is currently predicated on an expensive sediment removal program that must be performed every four years within a 1.2 mile reach of lower Novato Creek at a cost of $1M+.  This approach is not economically or ecologically sustainable and this watershed program process seeks to reduce the scope and frequency of this sediment removal while maintaining the level of flood protection.  This program seeks to provide the County and its partner agencies, City of Novato, North Marin Water District and the Novato Sanitary District, with alternatives that reduce sediment input from upstream sources and rely on the inherent ability of Novato Creek to scour its channel and transport more sediment to the Bay.

Bank erosion along Novato Creek is extensive above Grant Avenue. This reach exhibits active erosion and many property owners are requesting a comprehensive approach to stabilization work.  This study would provide the modeling tools to assess long term solutions that are consistent with work completed to date and that would improve habitat conditions. 

Stakeholder Outreach

The watershed program will utilize a collaborative, iterative process to develop an integrated flood protection and habitat restoration program.  The Marin County Board of Supervisors recommended establishing stakeholder committees at three levels to support community outreach and to provide overall program direction (a complete list of committee members is included at end of this document).  A broad community outreach program is also recommended.

Community outreach will be developed around these key messages:

  • Working at the watershed scale acknowledges the mutually dependent interactions and linkages between our ridgetops, the valley floor, creeks, wetlands and San Pablo Bay. 
  • The watershed approach acknowledges the need to work collaboratively to identify solutions to reducing flood hazards, maintain local water supply, recycled water operations, and improving fish and wildlife habitat.
  • Implementation at the watershed scale takes time and is implemented in tandem with both public and private projects and the maintenance and rehabilitation of aged existing infrastructure.

Description of Watershed Stakeholder Committees

Policy Advisory Committee - This group of elected officials is comprised of the District County Supervisor, two representatives from the participating city council and the Board of Directors of the participating agencies. This committee provides policy input on program direction and community issues and will meet 1-2 times per year.

Operations and Finance Committee - The participating District managers and/or city manager and the Marin County Public Works director will use these meetings to evaluate progress and prioritize funding strategies and will meet 3-4 times per year.

Technical Working Group (TWG) - This group will include staff of participating State, Federal and local regulatory and participating agencies and community members with a science and technical background.  The group will be responsible for the review of watershed products and provide input on issues, needs and watershed priorities.  This group will include conservation and watershed groups, homeowners’ associations and other technical experts within their respective watersheds.  This group will meet at least quarterly to provide input and to review the development of work products

Community Outreach
Targeted community meetings, presentations at various local boards and homeowners associations and utilization of the watershed program website ( will support communication to the community at large.  The program website provides dedicated information about the watershed and is regularly updated with notices about workshops, meetings, proposals and projects.

Project Description and Outcomes
Novato is home to the Flood Control District’s largest flood control zone and the largest flood control project in the County was completed in 2006.  In Novato, the District has commitment and financial support from all the agencies representing flood control, stormwater, water supply and recycled water as the County of Marin, the City of Novato, North Marin Water District, and the Novato Sanitary District have agreed to partner on this process.  However, infrastructure in the lower reaches is aging, the lower channel must be dredged every four years at a cost of $1 million, bank erosion is extensive on the main stem of Novato Creek and the 1984 flood fee sunset years ago.  Currently, the District collects maintenance fees ($9/parcel for single family homes) that generate about $250,000 annually.  This fee was approved by the voters in 1984 and is scheduled to be collected in perpetuity.

This program will seek opportunities watershed wide to improve our operations and maintenance in a manner that is informed by sea level rise projections while we identify alternatives that would improve the creek’s ability to transport sediment to the bay.  The process considers the restoration of watershed health and function as a basic tenet to ensure our projects are eligible for the broadest range of funding at the State and Federal levels.

This phase of the program will produce planning tools to guide the development of viable flood reduction alternatives:

  • Hydrology and hydraulics (H&H) study
    This deliverable will provide a unified hydrology and hydraulics model of Novato Creek and limited major tributaries, storm drain modeling for the Nave Gardens neighborhood, hydrologic modeling of the Novato Creek watershed and the development of conceptual project alternatives modeled for their benefits (including sea-level rise scenarios), Technical input will be provided via the technical work group.  A RFP was released in October.  We received 11 proposals and have short listed four.  Status: Contract awarded to KHE (Kamman Hydrology & Engineering)
  • Alternatives Analysis
    This deliverable will provide criteria and evaluation of three alternatives that support multiple benefits such as flood protection, water quality improvements and habitat restoration.
  • GIS-based mapping and database development
    Staff will use existing GIS data (publicly-owned parcels, existing creek restoration sites, STRAW sites, stream data, fishery data) to develop a watershed-scale database and maps to assist with project prioritization.  Status: Ongoing

Proposed Budget



Watershed Hydraulic Study and Alternatives Analysis 




HEC-HMS Hydrology Model   


Creek habitat assessment   


Outreach and Stakeholder process  






County of Marin  


City of Novato 


North Marin Water District    


Novato Sanitary District        





Watershed staffing

Roger Leventhal, Associate Engineer

  • Project Manager, manages KHE (consultant) hydraulics study, develop hydrology model for Novato Creek Watershed.  Responsible for review of hydraulic modeling products and for providing input into the development of alternatives.

Chris Choo, Senior Planner

  • Manage contracts and track consultant budget.  Coordinate meetings with Technical Working Group and public outreach through the website.

Laurie Williams, Senior Planner

  • Develop GIS database to support project planning and prioritization.  Work with contractors to provide DPW data and to incorporate contractor datasets into Public Works databases.  Prepare maps for website and stakeholder meetings.

Liz Lewis, Principal Planner

  • Manage overall schedule, deliverables, and budget and coordinate communication with partners and County Departments.  Coordinate financial strategy with partners.

Watershed Overview

The Novato Creek, located at the northwestern extent of San Pablo Bay, is the largest watershed in eastern Marin County.  Its creeks flow eastward through oak and bay forests, grasslands, the City of Novato, and into San Pablo Bay near the mouth of the Petaluma River.  The basin is 45 square miles and the main drainage in the watershed is Novato Creek; Novato Creek joined by six major tributaries along its 17 mile length: Leveroni, Bowman Canyon, Warner, Arroyo Avichi, Arroyo de San Jose, and Simmonds Slough.

Watershed History

Human settlement

Miwok and Pomo people were the earliest residents of the watershed.  Olompali, the site of a significant Miwok village, is located at the southern base of Mt. Burdell.  In 1839 Mexican land grants established Rancho Novato.  Grazing brought a host of invasive annual grassland plants that eventually dominated the deep-rooted native perennial grasses and altered runoff rates.

By 1856 extensive apple orchards occupied the valley floor and many of the creeks had been channelized for irrigation.  The tidal marshlands had also been diked and drained for agriculture (primarily oat-hay production) by the middle of the nineteenth century.  Laurel Collins (1998) notes that at this same time, the marshlands were actually extending into the bay due to massive sedimentation from hydraulic mining in the Sierra Nevada.  In the 1880s the creek was dredged to make way for schooners bound for San Francisco.

The town of Novato covers 49% of the watershed area and occupies former grassland, oak woodland, and savanna areas.  Novato, one of the four townships in existence when Marin County formed in 1850, was incorporated in 1960.  The population grew sharply after the railroad was built.  Ground was broken for Hamilton Air Force Base in 1932 and dedicated in 1935 (the base was decommissioned in 1974, and designated as a historic district in 1988).  Because Novato was one of the last cities in Marin to be developed, it grew rapidly between 1970 and 1990.


Watershed Today

Changes to Watershed Processes

The Novato Creek watershed’s channel network has been altered from its historic natural conditions.  The channels we see today reflect those alterations and many of the channels are actively in transition to a more stable configuration.  The majority of the channels are narrower than expected for the watershed size and rainfall and urbanization has likely increased the timing and magnitude of peak runoff events such that more water flows to the creek at a quicker rate (Questa, 2007 1).

Extensive bank erosion indicates that the channels are in a widening phase.  Sediment production in the watershed occurs due to upslope processes such as landslides and gully development, as well as channel bed incision and bank erosion.

The mainstem of Novato Creek and its major tributaries are all highly entrenched within the city limits and are constrained by development on the banks.  Channels in the upper watershed are still incising and are expanding headward into hillside swales.

The stream and tide channels in the lower reaches of the watershed are managed for flood conveyance and navigation and no longer function optimally for sediment transport.  Sediment aggradation is occurring in the lower reaches as a natural process to re-establish a natural channel configuration based on hydrology, slope, and sediment supply dynamics.

Habitat Types



The Novato Creek watershed supports a diversity of communities— from mountainous and hilly headwaters to saltwater and brackish-water marsh along the bay.  According to the 1999 Upland Habitat Goals Project, the lower marsh habitats represent some of the largest remaining tidally influenced habitats in the bay region supporting abundant waterfowl populations.  Despite being one of the driest drainages in Marin County, the watershed supports both rearing and spawning habitat for steelhead.  Agricultural baylands within the Novato Creek watershed provide seasonal wetland habitat for migratory waterfowl and shorebirds and this watershed also contains oak woodlands that provide habitat for terrestrial wildlife species.

The watershed is composed primarily annual grasslands interspersed with oak-bay woodland and oak savanna in the upper watershed.  Small patches of northern coastal scrub occur within the woodlands and serpentine outcroppings occur at the upper elevations in the northern watershed.  In the lower watershed, oak woodland and oak savanna become more prevalent.  According to the Novato General Plan, the best developed riparian communities occur in the upper watershed along Novato Creek and Arroyo San Jose.

One of the best examples of an intact riparian community within the watershed is at O’Hare Park at Novato Road and San Marin.  In this area, the riparian plant community is structurally diverse and supports a mixture on native species and large woody debris is left in place by the City of Novato enhancing instream habitat.

The lower reaches of the watershed adjacent to Novato Creek and east of Highway 101 support saltwater marsh and brackish-water marsh; both are subject to tidal action.  Freshwater seasonal wetlands occur in areas that were once historical baylands.  These areas have been diked off to provide agricultural land and now support oat hay production.

Fish and Wildlife

The Novato Creek watershed supports a number of special status plants and animals.  Of particular interest are the occurrences of wetland-adapted species along Rush Creek and lower Novato Creek wetlands.  Noteworthy species include San Pablo song sparrow, California black rail, saltmarsh common yellowthroat, and California clapper rail.  Western pond turtles 2 (Fawcett 2000 3) and naturalized bullfrogs (ESA 2003 4) are known to occur in Novato Creek.



The Novato Creek watershed is known to support 10 extant fish species (6 native and 4 introduced).  Native species include California roach, Sacramento pikeminnow, Sacramento sucker, steelhead, threespine stickleback, and Prickly sculpin.  Introduced species include rainwater killifish, western mosquitofish, striped bass, and green sunfish.  Historically, the watershed supported native tidewater goby; the last collection occurred in 1945 (Leidy 2007 5).  Fawcett (2000 and 2006 6) also notes the presence of non-native bluegill, largemouth bass, brown bullhead, chameleon goby, and inland silverside.

Salmonids (steelhead and Chinook salmon) are also found within the Novato Creek watershed. According to Supervising Fisheries Biologist with DFG, George Neillands, Chinook salmon are likely strays from the Sacramento River system. A net pen release site for the Sacramento River Chinook is located in Tiburon, which could result in fish moving into Marin streams.

There are no reported occurrences of California red-legged and foothill yellow legged frogs within the watershed (CDFG 2008 7).

Heron and egret nesting colonies have been monitored by Audubon Canyon Ranch since the early 1990s (Kelly, et al., 2006 8; E. Condenso personal communication, May 15, 2008).  There are two active and one inactive heronries within the greater Novato Creek watershed.

Avian surveys were conducted from Diablo Avenue to Grant Avenue during the 2006 nesting season as part of the Novato Flood Control Project (Phase VIII) (ARA 2006).  65 avian species were detected over 1,300 meter reach, 27 confirmed nesting or thought to be nesting on site, and additional 12 suspected.  Noteworthy species include Great blue heron, Cooper’s hawk, Allen’s hummingbird, purple martin, oak titmouse-nesting, Nuttall’s woodpecker – nesting.

Human Habitation and Land Use

Land UseImperviousness

Land Use                                        Imperviousness

The development of Novato leveled off between 1990 and 2000 then increased— as a result, Novato was the fastest growing city in Marin in 2005 and is anticipated to continue to grow, reaching a projected population of approximately 63,000 by 2020.  Over the next 20 years the City expects greater growth in jobs than population, lowering the percentage of the population that commutes to other places for work.

Novato is actively engaged in downtown redevelopment with proposed development of commercial and residential uses and supporting infrastructure.  The Marin Countywide Plan identifies Novato as having the greatest growth potential in Marin for commercial and industrial development.

Land protection and restoration efforts in the watershed include the Hamilton Wetland Restoration project, Rush Creek and Bahia restoration projects, and planning by the City of Novato and Marin County Open Space District for preservation and land acquisition for trails.

1 Novato Creek Bank Stabilization Guidelines

2 Personal communication, M. Fawcett to L. Lewis

3 Novato Creek EIR - Phase VIII flood control project

4 Ecology, Assemblage Structure, Distribution & Status of Fishes in Streams Tributary to the San Francisco Estuary

5 Letter: Novato Flood Control Project, Phase VIII; Fish Salvage and Relocation

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

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