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Lower Lagunitas Creek Habitat Restoration Project

Project URL link
Sponsoring Agency Marin Municipal Water District
Subregions ('North Bay',)
Counties Marin
Watershed Tributary
Public or private land? ()
Location (lat/lon) 38.0503, -122.7602
Start Date 01/01/2015
End Date 09/30/2019
Location Description Lagunitas Creek, Marin County. The project area is a 4.1-mile reach of the mainstem of the creek, and the associated tributaries, located downstream of Kent Lake (see attached project location map.)
Lower Lagunitas Creek Habitat Restoration Project

This project will implement restoration work along 4 miles of Lagunitas Creek, to benefit endangered coho salmon and threatened steelhead trout. The work will enhance overwinter and floodplain habitat, in the mainstem of the creek, and reduce sediment loading and improve fish passage by ”storm-proofing” tributary stream crossings along the Cross Marin Trail, in the same reach. This project expands two existing IRWMP projects:  Lagunitas Creek Winter Habitat Enhancement Implementation, and Lagunitas Creek Sediment Reduction and Management Project.

Project elements include 1) constructing engineered log jams to enhance base flow and floodplain habitat in the creek and 2) upgrading undersized culverted road crossings of tributaries to the creek. Project benefits are: providing flow refuge for juvenile and adult salmonids during winter storms, enhancing overwinter rearing habitat for juvenile coho and steelhead, increasing the creek’s carrying capacity for coho and steelhead,  sorting and storing fine sediment in the floodplain, strictly minimizing persistent and catastrophic erosion, reducing fine sediment loading into Lagunitas Creek and its tributary streams, improving fish passage in selected tributaries to Lagunitas Creek, improving water quality, and improving streambed habitat, all for the benefit of coho salmon and steelhead trout populations.

All work will be done at sites identified in existing assessments and design reports that highlight the need for such work. Work along the Cross Marin Trail will also safeguard a major public water supply transmission line and repair or maintain recreational access within National Park Service and California State Parks land.

 

Drinking Water Supply
Water Quality Improvement
Water Reuse/Recycling
Stormwater Improvements
Groundwater Benefits
Infiltration
Habitat Protection and Restoration
Flood Protection
Drinking Water Supply: This project addresses water supply reliability by reducing potential vulnerabilities associated with a major water supply distribution pipeline. Water Quality Improvement: This project will reduce sediment input to creeks and enhance floodplain sediment storage, addressing goals and objectives identified in the State's Lagunitas Creek Sediment TMDL. Stormwater Improvement: The project will implement road drainage improvements by sizing them for the 100 year storm, thereby reducing turbidity and other adverse impacts from stormwater flows from these roads. Habitat Protection and Restoration: The project will enhance overwinter habitat for coho salmon and steelhead trout in the mainstem and adjacent floodplain of Lagunitas Creek. The project will improve habitat for endangered salmonid species by reducing fine sediment loading to fish bearing streams and, in some cases, removing barriers to fish passage.

Part 2 - Detail

Lagunitas Creek supports the largest and most stable population of endangered coho salmon in Central California, as well as a robust population of threatened steelhead trout. This project will restore habitat for these species by enhancing overwinter habitat and reducing fine sediment input to the creek. These are two critical implementation strategies identified to support and encourage recovery of coho and steelhead. The restoration work is identified for implementation in the Lagunitas Creek Stewardship Plan (2011, MMWD), the State and federal coho salmon recovery plans, and the State’s Sediment TMDL plan for Lagunitas Creek. This project expands two previously submitted IRWMP projects:  Lagunitas Creek Winter Habitat Enhancement Implementation, and Lagunitas Creek Sediment Reduction and Management Project.

The project is detailed in two recently completed studies. Winter habitat enhancement construction sites were identified in the Lagunitas Creek Salmonid Winter Habitat Enhancement Assessment Report (2013), and then the Basis of Design Report for the Lagunitas Creek Salmonid Winter Habitat Enhancement Project (2013) provided 100% construction designs and specifications for winter habitat enhancement work at nine specific sites. Sediment reduction work was identified in the Lagunitas Creek Watershed Sediment Source Site Assessment (2013), which specifies treatment recommendations and sediment savings for each identified road erosion site, including 60 sites along the Cross Marin Trail. An initial phase of the winter habitat enhancement work (at four sites) has been awarded 2014 California Department of Fish and Wildlife, Fisheries Restoration Grant Program funding. An initial phase of the sediment reduction work (at three major sites) is currently being implemented, funded under the Bay Area’s Proposition 84, Round 2 Implementation Grant. The project proposed here is a second phase of winter habitat enhancement and sediment reduction work, to be conducted in proximity to the phase one efforts, in and at tributaries to Lagunitas Creek.

Winter Habitat Enhancement

Survival of coho and steelhead in the creek can be improved by enhancing rearing and high flow refuge areas. This implementation project will install Large Woody Debris structures, as engineered log jams, to reconnect the floodplain with the main channel, to be used by over wintering juveniles and spawning adults. This will allow for higher densities and greater carrying capacity of salmonids through the winter. Reconnecting the floodplain will also allow for fine sediments in the flood waters to settle out and be stored in the floodplain, to improve water quality.

This project will implement the construction of up to four winter habitat enhancement features, which were previously identified and designed in the winter habitat assessment. The assessment produced 100% engineered design drawings, specifications, and construction cost estimates for the specific sites where habitat enhancement will be implemented. The 100% design drawings will be used for environmental review and permitting, contractor bidding, and site construction.

Sediment Reduction
Sedimentation, particularly by fine sediments, has been identified as being detrimental to the habitat of Lagunitas Creek for coho and steelhead. The State Water Quality Control Board has identified Lagunitas Creek as being impaired by sediment and has adopted a sediment TMDL for Lagunitas Creek. This project will implement actions aimed at reducing fine sediments from entering the creek, leading to enhanced water quality and streambed conditions of Lagunitas Creek. In addition, project work will strengthen the route along which the Marin Municipal Water District’s Nicasio Transmission Pipeline, a major public water supply transmission line, runs.

Project work will be conducted collaboratively on MMWD, State Park, and National Park Service (NPS) lands, as well as some private properties within the watershed, in collaboration with the Marin RCD. The above referenced Lagunitas Creek Watershed Sediment Source Site Assessment has identified approximately 300 sediment source sites on unpaved roads in the watershed downstream of reservoirs. This includes 60 sites along the Cross-Marin Trail which is the route of MMWD’s Nicasio Transmission Pipeline and an important recreational trail. This IRWMP project will implement improvements to the Cross Marin Trail to strengthen the transmission line and stabilize this recreational trail. The work will address both chronic and catastrophic sources of sediment. Also, gravel management actions, as identified from an MMWD-led, in stream gravel assessment, will be implemented in order to increase the gravel and cobble fraction of the streambed.

This project work is included in the Lagunitas Creek Stewardship Plan. Also, winter habitat enhancement and sediment reduction in Lagunitas Creek have been identified as important recovery actions in the State's Recovery Strategy for California Coho Salmon as well as the federal Recovery Plan for Central California Coastal Coho Salmon. In addition, fine sediment reduction is a focus of the State's Lagunitas Creek Sediment TMDL.

Project Scalability

The scope of this project, and the grant request amount, are scalable. Total estimated costs to implement the winter habitat enhancement and sediment reduction work identified for this reach of Lagunitas Creek, is $5 million. Initial phases of work already funded will accomplish $1.5 million in work, leaving $3.5 million unfunded. This proposal requests $1.5 million and will accomplish $2 million in work. By adding or reducing the number of project sites implemented, the proposed grant request and cost share can be scaled upwards to $3.5 million or downwards to $1.0 million.

Disadvantaged Community: This project does not provide benefits specifically for a DAC; the project will benefit the Lagunitas Creek watershed in Marin County, California and the Bay Area region in general.

DAC

This project will not provide specific benefits directly for a disadvantaged community. The project will benefit the region and Lagunitas Creek in general, rather than a specific DAC.

 

 

False
Regional priorities addressed by this project include regional water supply reliability/long-term sustainability; health of the Bay and creeks; sediment management; and fisheries restoration for coho salmon and steelhead recovery. Lagunitas Creek supports the largest and most stable population of endangered coho salmon in Central California; it also supports a robust population of threatened steelhead trout. The Lagunitas Limiting Factors Analysis (Stillwater Sciences 2008) identified winter habitat as the limiting factor for both coho salmon and steelhead populations in the Lagunitas Creek watershed. Fall juvenile and spring smolt survey data indicate dramatic declines in the numbers of juvenile coho during the winter months. It is hypothesized that winter habitat in Lagunitas Creek is limited during base flow to bank-full periods. Sedimentation, particularly by fine sediments, has been identified as being detrimental to the habitat of Lagunitas Creek for coho and steelhead. Roads are a major source of both chronic and catastrophic sediment loading to fish-bearing streams. MMWD has major water supply transmission pipelines running under some of the roads in the Lagunitas watershed. The Sediment Site Source Assessments estimates that up to 56,400 cu.yds of sediment (over 20,000 cu.yds. on the Cross Marin Trail alone) could be prevented from entering Lagunitas Creek and its tributaries by implementing the recommended sediment reduction work. The State Water Resources Control Board has identified Lagunitas Creek as being impaired by sediment and has adopted the Lagunitas Creek Sediment TMDL which calls for implementing sediment reduction from roads and also to reconnect the mainstem of Lagunitas Creek to its floodplain, and install large wood, to sort and store fine sediment. This project will implement actions aimed at increasing winter habitat and reducing fine sediments from entering the creek, leading to enhanced habitat, water quality and streambed conditions of Lagunitas Creek. In addition, some of the project work will secure the route along the Marin Municipal Water District’s (MMWD’s) Nicasio Transmission Pipeline, a major public water supply transmission line. The federal Recovery Plan for Evolutionarily Significant Unit of Central California Coast Coho Salmon Final Plan (National Marine Fisheries Service , 2012) includes this task for coho recovery: “Conduct rehabilitation activities that restore channels, floodplains and meadows to extend the duration of the summer flow and provide refuge from high winter flows (Evaluate the Tocaloma reach of the lower Lagunitas mainstem)”. This project is within the Tocaloma reach of lower Lagunitas Creek.  

Coho salmon in Central California are on the brink of extinction; not implementing this project will not provide the habitat enhancement and sediment reduction needed to help recover the population, not only for Lagunitas Creek but for all of Central California.

A failure of culverts at Lagunitas Creek tributary crossings of the earth and road conveying the District's water supply transmission pipeline could have a significant impact on water supply to large portions of Marin County.

Regional priorities addressed by this project include regional water supply reliability/long-term sustainability; health of the Bay and creeks; sediment management; and fisheries restoration for coho salmon and steelhead recovery. (Additional narrative regarding specific manner in which this project addresses regional priorities can easily be provided upon request.)

i. Water Supply (conservation, recycled water, groundwater recharge, surface storage, etc.)

The project work will strengthen the route along which the Marin Municipal Water District’s (MMWD’s) Nicasio Transmission Pipeline, a major public water supply transmission line, runs, by strengthening the earth supporting the pipeline at culvert crossings and other sediment reduction sites. This will provide water supply reliability for MMWD's customers in Marin County.

 

ii. Water Quality

The project will support the State's Sediment TMDL for Lagunitas Creek by reducing fine sediment loading to streams supporting endangered coho salmon and threatened steelhead. Sediment reduction will enhance habitat for the benefit of coho and steelhead by resulting in increased pool habitat and improved sediment quality at critical spawning riffle habitats. Sediment loading reductions will also reduce turbidity and improve water quality conditions for all aquatic life in Lagunitas Creek. The project will also directly support the Sediment TMDL by installing large wood and reconnecting the mainstem channel to its floodplain, to sort and store fine sediment.

 

iii. Flood and Stormwater Management

The project will implement road drainage improvements by sizing them for the 100-year storm, thereby reducing turbidity and other adverse impacts from stormwater flows from these roads.

 

iv. Resource Stewardship (watershed management, habitat protection and restoration, recreation, open space, etc.)

This project provides Resource Stewardship benefits as it will result in habitat protection and restoration in several aspects: 1) it will implement the construction of up to four winter habitat enhancement features for the benefit of endangered coho salmon and threatened steelhead. 2) The project will reduce fine sediment loading to streams supporting endangered coho salmon and threatened steelhead. 3) The project will also enhance floodplain sediment storage, addressing the primary goals and objectives identified in the State’s Lagunitas Creek Sediment TMDL. Sediment reduction will enhance habitat for the benefit of coho and steelhead by resulting in increased pool habitat and improved sediment quality at critical spawning riffle habitats. Sediment loading reductions will also reduce turbidity and improve water quality conditions for all aquatic life in Lagunitas Creek and, in some cases remove barriers to fish passage.


The project will have a public recreation benefit for hikers, bicyclists, and equestrians, who use the recreational roads in the watershed. The road drainage improvements will also improve the road surfaces to more stable road beds and provide recreation reliability with the roads being open and passable.

 

Benefit/Cost Ratio

As noted above, Phase I of the sediment reduction work along the Cross Marin Trail is currently underway and was included in the Bay Area’s Proposition 84, Round 2 IRWM Implementation Grant. A rigorous benefit/cost analysis was conducted during the proposal development process, which resulted in establishing a benefit/cost ratio of 3.09 for this project. As the sediment reduction work included with this current concept proposal is virtually identical in nature (just at different sites located along the stream reach) to the Phase I work, it is reasonable to assume the sediment reduction work proposed here would also achieve a 3.09 benefit/cost ratio. Phase I of the winter habitat enhancement work proposed here is receiving funding from the California Department of Fish and Wildlife’s Fishery Restoration Grant Program. A detailed benefit/cost analysis has not been conducted or required for the winter habitat enhancement aspect of this proposed project, however the benefits are similar, and the costs are similar enough to the sediment reduction work costs and benefits, that we can assume a high benefit/cost ratio for this proposed project, likely close to the 3.09 benefit/cost ratio already determined, as described above.

 

Integration

This project presents a high degree of up-front integration as it addresses priorities associated with several Functional Areas, including Water Supply/Water Quality, Stormwater/Flood Control, and Watershed/Habitat. As described above, the project will contribute measurably to water supply reliability, water quality improvement, watershed habitat restoration, endangered species protection, as well as providing stormwater and recreation benefits.

False
False
False
Increases Water Supply Reliability
Advances/ Expands Conjunctive Management of Multiple Water Supply Sources
Increases Water Use and/or Reuse Efficiency
Provides Additional Water Supply
Promotes Water Quality Protection
Reduces Water Demand
Advances/Expands Water Recycling
Promotes Urban Runoff Reuse
Addresses Sea Level Rise
Addresses other Anticipated Climate Change Impact (e.g. through water management system modifications)
Improves Flood Control (e.g. through wetlands restoration, management, protection)
Promotes Habitat Protection
Establishes Migration Corridors
Re-establishes River-Floodplain Hydrologic Continuity
Re-introduces Anadromous Fish Populations to Upper Watersheds
Enhances and Protects Upper Watershed Forests and Meadow Systems
Other (Please Describe)
Increases Water Use Efficiency or Promotes Energy-Efficient Water Demand Reduction
Improves Water System Energy Efficiency
Advances/Expands Water Recycling
Promotes Urban Runoff Reuse
Promotes Use of Renewable Energy Sources
Contributes to Carbon Sequestration (e.g. through vegetation growth)
Other (Please Describe)
(low) - (high)
Drought Preparedness
Use and Reuse Water More Efficiently
Climate Change Response Actions (Adaptation to Climate Change, Reduction of Greenhouse Gas Emissions, Reduce Energy Consumption)
Expand Environmental Stewardship
Practice Integrated Flood Management
Protect Surface and Groundwater Quality
Improve Tribal Water and Natural Resources
Ensure Equitable Distribution of Benefits
Reduce Reliance on the Bay-Delta
Reduce Water Demand
Improved Operational Efficiency and Transfers
Increase Water Supply
Improve Water Quality
Improve Flood Management
Practice Resources Stewardship
Other Strategies (Please Describe)
Groundwater Management Plan
Urban Water Management Plan
Water Meter Requirements
Groundwater Monitoring Requirements
AB 1420 Compliance
BMP Compliance
CEQA Compliance
Water supply reliability, water conservation and water use efficiency
Stormwater capture, storage, clean-up, treatment, and management
Removal of invasive non-native species, the creation and enhancement of wetlands, and the acquisition, protection, and restoration of open space and watershed lands
Non-point source pollution reduction, management and monitoring
Groundwater recharge and management projects
Contaminant and salt removal through reclamation, desalting, and other treatment technologies and conveyance of reclaimed water for distribution to users
Water banking, exchange, reclamation and improvement of water quality
Planning and implementation of multipurpose flood management programs
Watershed protection and management
Drinking water treatment and distribution
Ecosystem and fisheries restoration and protection
Reduced Reliance on the Bay-Delta
Projects that directly address a critical water quality or supply issue in a DAC
Urban water suppliers implementing certain BMPs as on page 17 of Guidelines
Be designed to manage stormwater runoff to reduce flood damage (PRC §5096.827)
Be consistent with the applicable Regional Water Quality Control Plans (Basin Plans) (PRC §5096.827)
Not be a part of the State Plan of Flood Control (SPFC) (PRC §5096.827)

Project team

Part 3 - Benefits