Overview Links Related Efforts Documents Meetings Napa Sonoma Marsh Restoration Project

Restoration Objectives

Preliminary Habitat Restoration Goals and Objectives
for the Napa-Sonoma Marsh Restoration Feasibility Study and EIR/EIS

California Coastal Conservancy
California Department of Fish and Game
U.S. Army Corps of Engineers
July 21, 2001



The U.S. Army Corps of Engineers, with the California Coastal Conservancy as the non-federal sponsor, is conducting a Feasibility Study and preparing an EIR/EIS which involves the technical analysis of alternatives for the restoration of nearly 10,000 acres of wetlands and associated habitats within the former Cargill salt pond complex in the North Bay, which is now owned by the California Department of Fish and Game, a partner in the study.

The habitat restoration goals and objectives for the 9,850 acres of former salt ponds and remnant slough and marsh habitat, now referred to as the Napa River Unit of the Napa-Sonoma Marshes State Wildlife Area, are outlined below.

The preliminary habitat restoration goals are separated into overarching goals that the project team has developed, a review of the North Bay regional goals from the Baylands Ecosystem Goals Report, and specific goals for the project site developed by the project team based upon the overarching goals and regional goals.

The preliminary habitat restoration objectives begin with a compilation of recommendations for the Napa River Area and Sonoma Creek Area from the Baylands Ecosystem Habitat Goals Report, constraints and opportunities present on the project site, specific objectives for habitat restoration on the project site, and the benefits of habitat restoration.

I. Preliminary Habitat Restoration Goals

Overarching Goals

  • Restore a mosaic of diverse habitats that will benefit a broad range of fish, wildlife, and plant species, including endangered and threatened species, fish and other aquatic species, and migratory shorebirds and waterfowl.
  • Restore natural, self-sustaining systems that can adjust to naturally occurring changes in physical processes, with minimum ongoing intervention.
  • Implement habitat restoration using adaptive management techniques.
  • Recognize constraints, which are a driver in determining restoration objectives.
  • Evaluate the restoration from a regional perspective, as not all regional objectives can be addressed within the project boundaries.
  • Protect special status species, to the extent possible, during the restoration process.
  • Restore habitats within the Napa-Sonoma Marshes that will change over time due to inherent dynamic characteristics of the estuarine system (in terms of seasonal as well as longer-term changes).
  • Phase the restoration within the project site and time the restoration in relationship with restoration projects throughout the Napa-Sonoma Marshes, particularly Cullinan Ranch and Skagg's Island, to reduce negative impacts (such as erosion of existing marshes and unintended breaching of levees) resulting from excessive change sin the tidal prism.
  • Accelerate the speed of habitat restoration by conducting salinity reduction of the former salt ponds as quickly as is safely possible.
  • Meet as many of the goals and objectives of the Baylands Ecosystem Habitat Goals Report as feasible, focusing on how this project's goals and objectives fit within the entire North Bay Region (see Regional Goals below and Regional Objectives on p.3).

Regional Goals for the North Bay

As stated in the Baylands Ecosystem Habitat Goals Report, (p. 97):

"The overall goal for the North Bay is to restore large areas of tidal marsh and to enhance seasonal wetlands. Some of the inactive salt ponds should be managed to maximize their habitat functions for shorebirds and waterfowl, and others should be restored to tidal marsh. Tributary streams and riparian vegetation should be protected and enhanced, and shallow subtidal habitats (including eelgrass beds in the southern extent of this subregion) should be preserved or restored.

"Tidal marsh restoration should occur in a band along the bayshore, extending well into the watersheds of the subregion's three major tributaries - Napa River, Sonoma Creek, and Petaluma River. Seasonal wetlands should be improved in the areas that are currently managed as agricultural baylands. All remaining seasonal wetlands in the uplands adjacent to the Baylands should be protected and enhanced.

"In much of this subregion, achieving the Goals will depend on the willingness of farmers to convert agricultural Baylands to tidal marsh and to allow the remaining areas to be managed as seasonal pond habitat.

" In total, the Goals for the North Bay subregion call for increasing the area of tidal marsh from the existing 16,000 acres to approximately 38,000 acres, and creating about 17,000 acres of diked wetlands managed to optimize their seasonal wetland function."

Project Site Goals

These goals for the Napa River Unit of the Napa Sonoma Marsh State Wildlife Area were developed by the Conservancy, Department of Fish and Game, and the U.S. Army Corps of Engineers, based upon the overarching goals for the project and the regional goals from the Baylands Ecosystem Goals Report.

  • In a phased approach, restore large patches of tidal marsh that support a wide variety of fish, wildlife, and plants, including:
  • special status mammals and water birds, specifically the salt marsh harvest mouse, California clapper rail, and black rail;
  • endangered fish, specifically Delta smelt, Sacramento splittail, steelhead trout, and Chinook salmon, and other fish species; and
  • aquatic animals, including the Dungeness Crab, and other benthic and planktonic invertebrates.
  • Ensure connections between the patches of tidal marsh (within the project site and with adjacent sites) to enable the movement of small mammals, marsh-dependent birds, and fish and aquatic species.
  • Restore tidal marsh in a band along the Napa River to maximize benefits for fish and other aquatic animals.
  • Manage water depths of ponds to maximize wildlife habitat diversity, with shallow-water areas for migratory and resident shorebirds and dabbling ducks and deep-water areas for diving benthivores.
  • Manage salinity levels in ponds to support a rich diversity of biota.
  • Break up unneeded levees to create refuges for roosting and nesting shorebirds.
  • Manage invasive plant species, as feasible.

II. Preliminary Habitat Restoration Objectives

Regional Objectives for the Napa-Sonoma Marsh

Below is a compilation of applicable recommendations for the Napa River Area and Sonoma Creek Area from the Baylands Ecosystem Habitat Goals Report, 1999, pp. 106-109.

  • Restore large areas of tidal salt marsh along both sides of the Napa River, including former salt ponds and Cullinan Ranch.
  • Restore a continuous band of tidal marsh along the entire shoreline of San Pablo Bay, particularly near the mouths of sloughs and major streams, and enhance existing marsh patches by improving tidal circulation.
  • North of Highway 37, restore a broad plain of tidal marsh on both sides of Sonoma Creek, including the portion of Skagg's Island west of Skagg's Island Road.
  • Enhance seasonal pond habitat on remainder of Skagg's Island.
  • Manage diked wetlands and seasonal wetlands in the adjacent uplands to improve seasonal ponding.
  • Establish managed marsh or enhanced seasonal pond habitat on diked baylands that are not restored to tidal marsh.
  • Where possible, enhance riparian vegetation and marsh/upland transitions and provide upland buffers.
  • Manage the remaining inactive salt ponds on both sides of the Napa River as salt pond or shallow, open water habitat to support waterfowl.
  • Enhance seasonal wetlands at the Mare Island dredged material disposal ponds to improve habitat for shorebirds.

Project Constraints and Concerns

Environmental Constraints

  1. Effluent discharge limitations
    1. Salinity
      1. Sloughs
      2. River
      3. Bay
    2. DO
      1. Sloughs
      2. River
      3. Bay
    3. Temperature
      1. Sloughs
      2. River
      3. Bay
    4. Other Salts/Metals
      1. Sloughs
      2. River
      3. Bay
    5. TSS/Sediment Load
      1. Sloughs
      2. River
      3. Bay
  2. Mixing zone restrictions around discharge location(s)
  3. Nutrient, DO, and heavy metals content of treated waste water relative to pond water, and temperature differential
  4. Entrainment of organisms in discharges and diversions
  5. Loss of existing habitat in the ponds/loss of existing food sources (e.g., brine shrimp) during salinity reduction
  6. Salinity constraints on "downgradient" ponds
  7. Protection periods for listed species including salmonids, Delta Smelt, Clapper Rail, Sacramento Split-Tail, and Long-Fin Smelt (e.g., salmonids: April - June)
  8. Solution rate of precipitated salts/metals
  9. Ability to adequately resolubilize precipitated compounds
  10. Presence of other metals, pesticides, in sediments and levees, etc.
  11. Permit conditions/ability to obtain permits (e.g., NPDES)
  12. Constraints on construction noise within 250 feet of clapper rail habitat (Feb 1 to Aug 31)
  13. Change in tidal prism with opening of ponds (i.e., rate at which ponds can be opened)
  14. Siltation rates in ponds opened up to tidal action/sediment budget for ponds
  15. Cullinan Ranch levee breach impact on Pond 3 levee

Environmental Issues/Concerns

  1. Non-native invasive species (primarily spartina)
  2. Predator management
  3. Erosion of existing marshes along sloughs (short term loss of endangered species habitat)

Engineering/Physical Constraints

  1. Access - most ponds are on islands not accessible by land-based construction equipment or water craft (water levels in sloughs are too low most of the time)
  2. Quantity of imported water available from Sonoma County Water Agency (SCWA), including seasonal variations and timing relative to project
  3. Condition and capacity of existing water intake/diversion/transfer/discharge structures
  4. Conditions of existing levees
  5. Locations of water intake and discharge points
  6. Solubilities of bittern salts
  7. Existing bathymetry/topography
  8. Evaporation rate/salt load of intake water
  9. Seismic risk (liquefaction, amplification of ground shaking)
  10. Highway 37
  11. Erosion of sloughs leading to levee erosion; erosion of levees leading to impacts on adjacent properties, erosion around power line piers

Engineering/Physical Issues/Concerns

  1. Salinity gradients between pond water (brine) and flushing water (mixing characteristics)

Economic Issues/Concerns

  1. Cost of water pipeline from SCWA
  2. Cost of water intake/discharge/transfer structures
  3. Managed habitat O&M costs

Schedule Issues/Concerns

  1. Lack of maintenance funding resulting in levee deterioration and increasing pond salinity
  2. Need to arrest habitat deterioration
  3. Need to reduce salt concentrations prior to levee failure
    • Erosion
    • Seismic Risk
  4. Other restoration projects (Sonoma Creek Flood Control Project, Cullinan Ranch, Skaggs Island, Guadalcanal)

Project Site Opportunities

  • Restore large tracts of connected tidal marsh, with a band of marsh along the Napa River.
  • Continue to manage shallow-water and deep-water muted tidal ponds which currently provide habitat and are feasible to maintain.
  • Maintain as salt ponds those ponds which have levees accessible for maintenance and low likelihoods of levee failure.
  • Manage the depths and salinities of salt ponds for waterfowl and shorebirds.
  • Restore tidal marsh in ponds which have levees that are not accessible for maintenance and/or high chances of levee failure.

Approximate acreage of Napa River Unit

Pond 1 354 acres 5%
Pond 1A 528 acres 7%
Pond 2 781 acres 11%
Pond 2A 561 acres 8%
Pond 3 1,314 acres 18%
Pond 4 960 acres 13%
Pond 5 771 acres 11%
Pond 6 755 acres 10.5%
Pond 6A 454 acres 6%
Pond 7 302 acres 4%
Pond 7A 290 acres 4%
Pond 8 102 acres 1.5%
TOTAL "ponds": 7171 acres 100%
Other (marsh, sloughs, levees): 2,679 acres  
TOTAL (DFG property): 9,850 acres  


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