Pine Gulch Creek Watershed Enhancement Project, Marin County

California Coastal Conservancy and Marin RCD


A state law was passed in 2004 (AB 2121) that required the State Water Resources Control Board (SWRCB) to adopt (by January 1, 2008) a policy to maintain in-stream flows in north coast streams from the Mattole River to San Francisco, and in coastal streams entering northern San Pablo Bay. The policy, termed the North Coast Instream Flow Policy, is meant to guide SWRCB in its administration of water rights in the region. It is also likely to serve as a model for balancing in-stream flows with water withdrawals in other regions of the state. The preparation of this policy continues and its status can be seen at:

In the meantime, there has developed a backlog of water permit requests in the North Coast. SWRCB estimates that there are 1,700 unpermitted ponds in the region in addition to over 300 water rights applications, including some that have been languishing for 10-15 years.

A project that combines irrigation ponds with stabilized in-stream flows, and that is thought to serve as a model for balancing interests, is the Pine Gulch Creek project in West Marin County. The shift in water rights contemplated in the project had progressed to public comment at the SWRCB by May 2009.

A landowner guidance manual is being prepared as a result of this project and should provide information about replicating the experience elsewhere in the state.


Located in west Marin County, the 7.5 square mile Pine Gulch Creek watershed provides habitat for federally listed Central California Coast coho salmon (Oncorhynchus kisutch) and Central California Coast steelhead trout (Oncorhynchus mykiss). In addition, coho salmon are listed as a candidate species under the California Endangered Species Act (CESA). Coho salmon are currently at six to fifteen percent of their abundance during the 1940s. Given this decline, and in light of the State Recovery Strategy’s primary objective of returning coho salmon to a level of sustained viability while protecting their genetic integrity, projects such as this with a high potential for recovering local populations of coho are a high State priority.

The Pine Gulch Creek Watershed Enhancement Project is a voluntary cooperative effort on the part of the participating organic farmers: Fresh Run Farms; Paradise Valley Farms; and Star Route Farms, whose historic riparian water use for crop production date back several decades. As a group, these Bolinas farmers form a vital component of West Marin agricultural production. Through this project, they propose to modify existing water operations to support sustainable agriculture and enhance aquatic habitat supporting coho salmon and steelhead trout.

The participants intend to increase stream diversion levels when flows are high, and reduce and even eliminate stream diversions when flows are low. Doing so requires adjusting water use from year-round direct diversions to seasonal appropriation and storage of water for later use (appropriative rights require a permit, but enable the holder to withdraw and store water for later use for a period of greater than 30 days). The proposed project includes appropriation of water to storage during the winter season, controlled riparian diversion between April and July 1, and no diversion between July 1 and December 15 of each year. This solution has been developed through consultation with the California Department of Fish and Game (CDFG), National Marine Fisheries Service (NOAA-Fisheries), and State Water Resources Control Board (SWRCB). As part of the project, the farmers are applying for appropriative water rights, and will dedicate their summer commercial irrigation riparian rights to in-stream flow for the benefit of fish habitat.

Site Description

Pine Gulch Creek is an approximately seven mile long perennial stream draining a watershed of about 7.8 square miles in western Marin County. Pine Gulch Creek is the principal source of fresh water to Bolinas Lagoon and probably contributes about one-half of the Lagoon’s freshwater inflow. Three miles of the creek are within the coastal zone. The portion of the stream within the coastal zone is partially within lands of the Point Reyes National Seashore, but the majority flows through the agricultural lands of Paradise Valley and the Pine Gulch Creek Delta. Upstream from the coastal zone, the creek flows entirely within lands of the Point Reyes National Seashore. This flow is especially important in the summer when the remaining tributary streams dry up or are reduced to very low flows. While the National Park Service manages 85% of the watershed area (primarily upstream), the remaining 15% of private lands include nearly 30% of the mainstem aquatic habitat known to support coho salmon and steelhead trout.

Project History

The project was originally conceived in 1998, prior to the return of coho salmon to the watershed and the petition to list coho salmon as a State endangered species in this area.

In 1998 the farmers had applied for streambed alteration permits for their water diversions. In response, the California Department of Fish and Game (DFG) staff recommended that the permits mandate the development of offsite storage ponds. Doing so would potentially compel the abandonment of riparian water rights, (and promote the development of appropriative water rights, thereby reducing diversions during low flow periods, while enabling the farmers to store peak flows at offsite locations for use during dry periods.

The farmers experienced their first procedural hitch when the California Fish and Game Commission found that coho warranted listing under the California Endangered Species Act in 2002. This special status of coho, a species recently returned to Pine Gulch Creek, complicated discussions regarding the farmers’ applications with regulatory agencies. Extensive conversations and negotiations with regulatory agencies ensued. The initial project concept, submitted for a Coastal Permit/Grading Permit to the County of Marin in September 2002, proposed construction of ponds –limited by policy to 30 days of storage- on each of the three participating farms. The intention of these ponds was to enable the three farmers to regulate the amount and timing of pumping from the creek, thus reducing instantaneous withdrawals during the low flow periods.

Extensive and continuing project discussions between the County, DFG water rights staff,NMFS, the farmers, and Point Reyes National Seashore (PRNS) staff, prompted several investigations into the optimum and most scientifically defensible in-stream flow level and project proposal. Participants sought to better understand what in-stream flow level would support coho salmon. Based on comments from the DFG, NOAA-Fisheries, and the public, the farmers modified the project significantly with the coho listing in mind.

A second procedural hitch occurred. In creating ponds, the farmers would likely attract, and increase populations of, red legged frogs, a federally listed species under the Endangered Species Act. Thus, the group needed to obtain a “safe harbor agreement” that would allow the farmers to “take” listed species in the course of conducting their agricultural operations. Generally, these agreements are only offered in instances where clear habitat improvements or benefits are achieved by the overall project. A “safe harbor agreement” was completed with the Fish and Wildlife Service with the assistance of Sustainable Conservation.

Project Description

The project includes an irrigation diversion and storage program, combining limited riparian withdrawals between April and June, and appropriative storage that will accommodate water needs for the growing season between July and December. All irrigation water diversions occur through screened pumps withdrawing water from the water column or intakes installed into the gravel of the stream bed. All water diverted through this project will be pumped into the ponds, and all irrigation of crops will be applied directly from the storage ponds. This will allow for lower diversion rates from the stream, further buffering the riparian diversion impacts. Because of limited storage, farmers would replace water used for irrigation with riparian water between April 1 and June 30. The farmers will dedicate all of their commercial riparian diversion between July 1 and December 15 to in-stream flow for the benefit of coho salmon and steelhead trout under the important but seldom applied California Water Code Section 1707 authority, which as revised allows the dedication of water rights to in-stream use for protection and enhancement of aquatic habitat. This dedication will be linked directly with the appropriative storage rights associated with the proposed ponds.

One of the most notable aspects of the in-stream flow enhancement effort is the coherent and comprehensive approach to addressing in-stream flow challenges. The participants in the Pine Gulch Creek project have, through careful study and analysis of alternatives, identified all existing sources of diversion, and quantified how their effort will have a measurable and beneficial effect upon the entire watershed, not simply at the point of a single diversion. Thus, the participants have addressed diversions comprehensively and coherently to guarantee in-stream flow for fishery habitat protection.

The project includes a series of monitoring measures that will be implemented within the watershed and by the farmers to ensure compliance. The monitoring measures include:
• Summer streamflow monitoring upstream of the Martinelli diversion
• Pump log and monthly operation summaries
• Ongoing streamflow monitoring below Olema-Bolinas Road Bridge
• Annual salmonid surveys conducted and reported through the NPS
• Annual Meeting schedule

Storage Plan

Appropriated water storage volumes have been calculated to insure that the farmers can meet their annual irrigation needs between July 1 and the end of the growing season. The completed designs will provide for the development of five storage ponds with a proposed storage of 61 acre feet, as seen in the following table:


Consistency with Basin Plan

The Water Board first adopted a plan for waters inland from the Golden Gate in 1968. After several revisions, the first comprehensive Basin Plan for the San Francisco Bay Region was adopted by the Water Board and approved by the State Water Board in April 1975. Repeatedly amended, the Tomales Bay watershed area is included in the Basin Plan by amendment. The Pine Gulch Creek project is consistent with the Basin Plan in that it protects many beneficial uses identified in the plan, such as protection of cold freshwater habitat, and removal of barriers to fish passage, as described below.

Cold freshwater habitat is a beneficial use protected in the Basin Plan. Uses of water that support cold water ecosystems, include preservation or enhancement of aquatic habitats, vegetation, fish, or wildlife, including invertebrates. Cold freshwater habitats generally support trout and may support the anadromous salmon and steelhead fisheries as well. Cold water habitats are commonly well-oxygenated. Life within these waters is relatively intolerant to environmental stresses, such as diversion of in-stream flows. The water quality provisions acceptable to cold water fish generally protect anadromous fish as well. However, particular attention must be paid to maintaining zones of passage. Any barrier to migration or free movement of migratory fish is harmful. Natural tidal movement in estuaries and unimpeded river flows are necessary to sustain migratory fish and their offspring. A water quality barrier, whether thermal, physical, or chemical, can destroy the integrity of the migration route and lead to the rapid decline of dependent fisheries. Water quality may vary through a zone of passage as a result of natural or human- induced activities. Fresh water entering estuaries may float on the surface of the denser salt water or hug one shore as a result of density differences related to water temperature, salinity, or suspended matter.


The participants engaged in this creative dedication of in-stream flow have succeeded in reaching a compromise over one of the most challenging resource conservation issues facing global communities: the use of water and its appropriate dedication in-stream for habitat conservation. The proposed actions by the participating farmers in Pine Gulch Creek will result in significant, long-term protection and management of aquatic habitat on private lands within the watershed. This cooperative arrangement by the farmers to improve their environmental and agricultural sustainability within this rich and unique watershed and ecosystem is precedent setting. The participants in this project are dedicated organic farmers who see this as a unique sustainable model of cooperation and successful resource management. This project represents significant adjustment and alteration of their current operations but is understood as a valuable and necessary step for the long-term sustainability of agriculture and salmonids in the watershed.