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06/26/98 Draft Report

Cover Letter

Project Participants



Chapter 1

Chapter 2

Chapter 3
Process for Establishing Goals

Chapter 4
Key Species and Communities

Chapter 5
Key Habitats of the Baylands Ecosystem

Chapter 6
Baylands Habitats, Past and Present

Chapter 7
Habitat Goals

Chapter 8
Technical Considerations for Habitat Restoriation

Chapter 9
Monitoring and Research

Chapter 10
Implementation Issues

Next Steps

Appendix A

Appendix B:

Appendix B:

Appendix B:

Appendix B:

Appendix B:
Other Birds

Appendix B:

Appendix C

PDF Version


San Francisco Estuary Baylands Ecosystem Goals Draft Report for Public Review June 26, 1998

Compilation of Focus Teams and Hydrogeomorphic Advisory Team Recommendations:
Mammals, Amphibians, Reptiles and Terrestrial Invertebrates Focus Team Recommendations


Plant Focus Team Recommendations
Fish and Aquatic Invertebrate Focus Team Recommendations
Mammals, Amphibians, Reptiles and Terrestrial Invertebrates Focus Team Recommendations
Shorebirds and Waterfowl Focus Team Recommendations
Other Birds Focus Team Recommendations
Integrating Abiotic Factors in the Goals Project: Tenets of the Hydrogeomorphic Advisory Team


The following is a compilation of the recommendations produced by each of the focus teams and the HAT. You will note that some of the terminology used in these reports differs from that used in the Goals Report. For example, some teams discuss regions and subregions that are defined differently, and some use different names for habitats. This is because the terminology used within the Project has evolved over time, and some has been developed specifically to facilitate presentation of the Goals.

In order to preserve the original intent of the focus team authors, no changes, other than minor formatting changes, have been made in the teams' reports. We believe the intent of their recommendations is made clear by the information contained in the reports.

Mammals, Amphibians, Reptiles and Terrestrial Invertebrates Focus Team Recommendations

This paper summarizes the MARI Focus Team's habitat recommendations. The recommendations are presented for each of the four Project subregions. For additional information regarding the MARI species that utilize the baylands and adjacent habitats, please refer to the individual species narratives that will be compiled in the Goals Project's Focus Team Species/Community Narrative Report.

Suisun Bay Region

While the taxa selected by the MARI Focus Team are genetically quite diverse, most are small and vulnerable to predation, disperse poorly, and have very limited tolerance for prolonged deep flooding. Therefore, while exceptional species will be discussed below, the following general recommendations are possible:

  1. preserve and/or create large areas (at least several hundred acres) of dense vegetative cover, centered around known populations of target species;

  2. connect these protected areas with corridors sufficient to allow periodic exchange of genetic material and repopulation in the event of local extirpation;

  3. to minimize disturbance (especially by predators) from outside the protected areas, design the protected areas with central areas far from the borders and/or provide buffer strips between the protected areas and potential sources of disturbance (including residential areas); and

  4. provide sufficient topographic relief within and/or adjacent to the protected areas to afford refuge during the highest flood water depths.

In addition, while high salinities are generally not detrimental to these taxa, so long as plant cover is not reduced, excessive freshness can be a problem if it promotes a mix of plant species (pepper grass, cattail, some Scirpus spp.) that displaces more favorable plant species (esp. pickleweed and other mid- to high-elevation halophytes). Therefore, 5) restoration projects should be designed to promote hydraulic conditions, including salinity regimes, that encourage vigorous growth of upper elevation halophytes. To the extent possible, this recommendation should be balanced by a general preference for projects and management schemes that 6) require minimal ongoing application of external energy (e.g. pumping, levee maintenance).

Another consideration, which is harder to evaluate, is the significance of tidal hydrology as an independent variable, apart from its influence on vegetation. While the vegetarian Salt Marsh Harvest Mice and California Vole have been trapped in abundance in diked or muted tidal marshes with typically tidal marsh vegetation, the insectivorous Suisun Shrew and Salt Marsh Wandering Shrew are apparently limited to "natural tidal salt and brackish marshes" [MacKay, Shellhammer, this project], and are not seen in diked marshes. It is not clear whether this is due to food availability or to other causes. In addition, although river otters have been observed in diked marshes with abundant crustaceans, Sea Otter, River Otter, Harbor Seal, and California Sea Lion are all essentially aquatic animals, presumably supported by open water and unrestricted channels. Thus, it is generally recommended that 7) restoration of full tidal action to diked marshes is desirable, where such restoration will not unacceptably reduce other wetland functions and values.

These considerations are not essentially different from those noted in the recommendations for other Regions, but their application in the Suisun Bay/Carquinez Strait Region can differ for a number of reasons:

  1. The generally fresher water conditions in the Suisun Bay area, compared to other Project Regions, means that fully-tidal, mid-elevation marshes often do not produce the plant communities associated with high densities of our target taxa, especially in the south-eastern reaches of the region. In addition, planning around salinity means and extremes is difficult, for salinity patterns depend not only on weather conditions, but also on legal decisions and the operation of specific pumps and dams. On the other hand, relatively low populations (i.e. little treated wastewater) and small local watersheds mean that there are few areas where local freshwater inputs are significantly affecting habitat.

    Desired plant communities, especially in the southeast, are often associated with high elevations relative to tidal datums and/or with muted tidal regimes, both of which encourage salt accumulation in soil.

  2. Most of the historically-tidal marshes of the Region have been diked, and many have subsided as a result. In addition, the Carquinez Strait is a significant bottleneck to heavy winter flows in the Sacramento or San Joaquin Rivers, and tidal elevations can be much higher than San Francisco or San Pablo Bays. Thus, while the subsidence is not generally so extreme that tidal restoration will result in permanent lagoons, marshes "restored" by dike breaching alone are often so low that flood stages can eliminate mammal populations, especially in sites without connections to adjacent vegetated uplands.

    Sediment accumulation following reintroduction of tides can restore pre-diking elevations, but access to sediment supplies varies considerably through the region, and marshes at the headwaters of long channels may build up very slowly. Marsh surfaces can also be artificially raised with dredge spoils, and the Montezuma Wetlands Project on the southeast corner of the Region is a major proposal of this type. Serious concerns about toxics and other potential problems have been aired, however, and it is unclear how widely this idea will spread.

  3. While many of the Region's marshes are very low, a relatively high number of them are associated with extensive, relatively undisturbed, adjacent uplands. This is a situation which can provide an unusually high potential for long-term survival of species, but only if these areas remain extensive and relatively undisturbed.

  4. The diked marshes of Suisun Bay are far more likely to be managed for relatively dense marsh vegetation cover than in other Regions, where diked marshes are usually managed for salt production, agriculture, flood control, and/or open water or mudflat habitats. While the current management regimes of Suisun Bay diked marshes are often not ideal to MARI target species, changes in water management can potentially promote MARI taxa without requiring complete restoration of free tidal action.

In light of these general recommendations and special conditions, we recommend the following habitat goals for the Suisun Major Subregion, based on promoting the long-term viability of the target taxa of the MARI Focus Team:

I. Suisun Marsh Minor Subregion

A. Protect and enhance the existing populations of target species along the periphery of the Subregion, by protecting, enhancing, and restoring appropriate hydrology and vegetation, in units of at least several hundred acres each, around the six known centers of small mammal population. This can be accomplished either by restoration of full tidal action or, in some cases, by modified water management on diked sites. By focusing initially on the areas outside Grizzly Island, we emphasize protection of areas with associated uplands, and we minimize risk to the central areas from future encroachment by residential or industrial development.

  1. Southwest Unit. The Benicia/Moth Ball Fleet shoreline has known or suspected populations of Salt Marsh Harvest Mouse, California Vole, Ornate Shrew, and River Otter; the highest average salinity in the Region; relatively low urban/industrial encroachment, and a large number of current restoration projects. These projects should be encouraged and additional tidal restoration/enhancement should occur to ensure the largest contiguous zone of tide marsh possible. Where restoration on full tidal action is not possible, changes in water management to encourage halophytes is desirable.

    One priority for restoration planning in this area is responding to the relative lack of undisturbed uplands adjacent to the marshlands, especially where Interstate 680 runs just above the edge of the marsh. High water refugia are essential for small mammals, and where undisturbed transitions to extensive uplands no longer exist, island creation or other selective placement of fill on parts of the marsh may be appropriate.

  2. Northwest Unit. The Cordelia Slough/Chadbourne Slough area has known or suspected populations of Salt Marsh Harvest Mouse, California Vole, Suisun Shrew, and River Otter; significant areas of adjacent uplands; and sparse residential or industrial development in the vicinity. While most of this area is currently managed for ducks or other (dry land) hunting, significant areas of good habitat for mice, voles, and shrews have been observed. Both tidal restoration and improved water management should be encouraged in this area, with emphasis on creating a contiguous habitat area of 1000 acres, with adjacent uplands.

    General restoration priorities in this area include improving water exchange under the Southern Pacific railroad line to maximize tidal exchange and minimize winter flooding, and restoring sufficient acreage to tidal action to maintain regional salinity in the face of projected increases in fresh water discharge into the head of Cordelia slough.

  3. North Central Unit. On the west side of the Potrero Hills, the Hill Slough, Rush Ranch, and Japanese Point areas provide extensive acreage of known and suspected populations of Salt Marsh Harvest Mouse, California Vole, Suisun Shrew, and River Otter, and some very good connections to undisturbed uplands. The proximity to rapidly developing areas around Fairfield makes protection of this areas a high priority.

    A restoration priority in this area is providing habitat continuity, given the steep topography and lack of marsh on the extreme west of the Potrero Hills. Parcels northwest of Hill Slough and west of Suisun Slough should also be protected.

  4. Northeast Unit. On the east side of the Potrero Hills, the Nurse Slough and Denverton Slough areas also provide extensive areas with known and suspected populations of Salt Marsh Harvest Mouse, California Vole, Suisun Shrew, and River Otter, and excellent connections to uplands, both in the Potrero Hills and on Bradmoor Island. Ideally, this unit would be extensive enough to connect to the North Central Unit with a continuous habitat band along the south side of the Potrero Hills this might require habitat protection on the extreme north of Grizzly Island. As with the North Central Unit, development pressures in adjacent areas make this a high-priority area.

    The channel water in this area has relatively low salinity. Therefore, a restoration priority is project design that encourages moderate salt accumulation in marsh soils.

  5. Southeast Unit. On the east side of Montezuma Slough are known populations of most target mammals and good connections to adjacent uplands. Development pressure is lower here than in the more northerly units, although a serious future concern. The Montezuma Wetlands Project proposes restoration of over 1000 acres of potentially high-value habitat in this area, using a combination of dredge spoils and natural sedimentation.

    In addition to potential difficulties with toxics in the sediment, restoration challenges include low channel salinities and subsided sites, and steep slopes on the west flank of Kirby Hill, which apparently rule out a continuous habitat corridor east of Montezuma Slough. Restoration priorities should include encouragement of desired vegetation, and restoration and protection of appropriate habitat on the east side of Grizzly Island.

  6. Channel Islands Unit. Most of Chipps, Ryer, and Roe Islands currently appears to be good habitat for target mammals. While adjacent uplands are lacking, and channel salinity is low, the large acreage and near-complete protection from development pressure (Ryer and Roe, in particular, are owned by the Navy) makes these good candidates for protection and enhancement, though with lower priority than the units described above.

B. Provide for habitat corridors for small mammal movement between the units described above. While potential connections have already been described between the North Central and Northeast, and Northeast and Southeast units, it is less clear how best to connect the Southwest and North Central population centers. If extensive areas of mammal habitat are protected in the Cordelia Slough area, than these can potentially serve as stepping stones. Other options include Joice Island or the northwest of Grizzly Island; either of which would require either extensive new levees, or the restoration of tide marsh vegetation on large parcels.

C. Enhance the management of the Grizzly Island complex, including Wheeler Island, Simmon's Island, and Van Sickle Island, for mammals. Large scale tidal restoration of the complex is not considered essential for preservation of the target species, and it is not clear that it would be desirable, given the subsidence and lack of adequate uplands on the islands, and the freshness of the surrounding water. On the other hand, relatively small-scale projects to enhance halophytic vegetation on site, to promote habitat corridors as discussed above, and/or to restore specific areas to tidal action should be supported.

II. Contra Costa North Shoreline Minor Subregion

A. Protect and enhance existing habitats and population centers, including restoration of tidal action as feasible. The degree of industrial, military, transportation, and residential development adjacent to these marshlands is high. On the other hand, the early development of industrial and military facilities on rocky zones along the coast probably discouraged residential expansion or management of wetlands for agriculture or waterfowl; therefore, the mammal populations of many of these marshes are high.

  1. West (Peyton/Pacheco) Unit. Abundant populations of Salt Marsh Harvest Mice and River Otters are known from the marshlands between I680 and Pacheco Slough; adjacent uplands are available with minimal disturbance; and the mean annual salinity is relatively high. Therefore, the potential for maintaining viable mammal populations justifies additional efforts to restore the undeveloped diked marshes in the vicinity to tidal action.

  2. West Central (Point Edith/Hastings Slough) Unit. Abundant populations of Salt Marsh Harvest Mice are known or suspected in much of this area, and the presence of Ornate Shrew is suspected. Some adjacent upland is available, salinities are moderate, a extensive restoration efforts are underway. Restoration priorities include responding to subsidence, rail lines with insufficient drainage, buried contaminants, and flood risk to adjacent structures.

  3. East Central Unit. The area from Port Chicago (Seal Bluff) to the Pittsburg power plant contains known and suspected populations of Salt Marsh Harvest Mouse, California Vole, Ornate Shrew, and River Otter. Protection from further development is strong, adjacent uplands are available, residential impacts are slight, and the feasibility of connecting the marshes is high.

    Constraints to restoration, which should be addressed, include buried contaminants, railroad lines, and existing land use (industry and a harbor). Protection of existing marshlands and adjacent uplands and buffers is important throughout the unit. In addition, tidal enhancement is feasible in areas, and where infeasible, improved water management can improve vegetation.

  4. East Unit. A relatively small area of shoreline between Pittsburg and Antioch support known populations of Salt Marsh Harvest Mouse, California Vole, and Ornate Shrew. While these populations should be protected, extensive enhancement is not justified, given the small acreage and the lack of adjacent undeveloped land.

  5. Channel Islands Unit. Brown's and Winter Islands are both large expanses of potentially good habitat for Salt Marsh Harvest Mouse, California Vole, and Ornate Shrew, with low development risk. Brown's Island is undiked and has not subsided; protection is probably adequate. Winter Island is diked and managed for waterfowl. Given its subsidence, the lack of uplands, and the freshness of the surrounding waters, enhancement for halophytes is a higher immediate priority than tidal restoration.

B. Provide for habitat corridors for small mammal movement between the units described above. The Peyton and Point Edith units are probably well-enough connected as long as the marshlands at the mouth of Pacheco Slough are protected. The most important corridors to promote would connect the Point Edith and East Central Units, across the relatively sparsely developed Tidal Area of the Concord Naval Weapons Station. In addition, the connection should be improved within the East Central Unit between the marshlands west and east of the General Chemical plant. The connections north of McAvoy Harbor and across Mallard Slough should be protected. Connecting the marshes west and east of Pittsburg is not feasible.

III. Carquinez Strait Minor Subregion

While mammal populations are known from Southampton and Martinez Waterfront Marshes, neither area is large enough and free enough of development to justify elaborate efforts to promote mammals. In addition, the steep rocky shorelines and the railroad along the Contra Costa shore argue against creation of wetland habitat corridors along the Strait.

North San Francisco Bay Region (San Pablo Bay)

The North Bay region begins on the west side of the Bay at Point San Pedro in Marin Country and extends north to include the Petaluma River and associated marshes north to the City of Petaluma. The Region extends east to include the Napa River and associated marshes south of the City of Napa. Turning south the Region includes the lands west of the Carquinez Bridge and continues to Point San Pablo. The majority of the development in this Region is concentrated along the Highway 101 corridor, in Vallejo at the mouth of the Napa River, and in Contra Costa County. This Region has a large amount of undeveloped land and has the greatest opportunities for marsh restoration of any of the Bay Regions.

After a great deal of discussion among the members of the MARI group it was decided that we would designate only parcels we believed were the minimum necessary to provide for the needs of the target species. Since the majority of the mammalian target species inhabit tidal salt marsh, parcels designated for restoration are generally adjacent to San Pablo Bay or to tidally influenced reaches of rivers that flow into the Bay. Undesignated parcels on our maps were left to allow the other focus teams flexibility to provide for the needs of their target species. Although we recognize the value of these undesignated parcels to the overall health of the North Bay marshes we felt that specific habitat designation by the MARI team was not necessary to achieve our goals.

The areas were selected in the North Bay were based upon several assumptions that the MARI team believed would best preserve the target species in perpetuity. A basic assumption that guided the recommendations was that large continuous patches of tidal salt marsh with existing populations of salt marsh harvest mice should be preserved. Where an existing salt marsh is insufficient to support viable mouse populations in perpetuity, it should be expanded to provide a large block of tidal marsh. Parcels were selected that would be large enough to develop the dendritic slough channel pattern and salt pannes characteristic of historic bay marshes. The wetlands should be large enough to require little or no maintenance once restored. Although corridors connecting the various tidal salt marsh blocks were discussed it was decided that, in the north bay, the need for corridors was not paramount due to the large amount of existing salt marsh and the potential for restoration of large self-sustaining blocks. Small, isolated wetlands in areas where a large block of tidal marsh does not exist and could not be restored were not recommended to be connected with corridors because we felt they were too small, even with connections, to sustain salt mouse harvest mouse populations in perpetuity. Additional considerations included the current land use and amount of existing infrastructure in the area resulting in only areas that could reasonably be restored to tidal action being recommended for restoration. The presence of adjacent uplands or the potential to create and preserve adjacent upland refuge habitat was another important consideration for the team when selecting the blocks of salt marsh for preservation and/or restoration. The transition habitat that provides refugial habitat during high tide events is extremely important to the long term viability of a tidal salt marsh for small mammal species. This upland transition/buffer habitat can also provide seasonal wetland values for other target species and its value cannot be overstated. We also included parcels that were already being restored or would soon be restored (Sonoma Baylands and Tolay Creek wetlands) whether we believed these parcels to be essential to the area or not.

Originally the North Bay was divided into five separate areas that we believe could independently sustain viable populations of salt marsh harvest mice, Suisun shrews, and San Pablo voles. The five areas were, beginning in Marin County and moving around the North Bay in a clockwise direction:

  1. the Hamilton/Bel Marin Keys wetlands, an area roughly north of Las Gallinas Creek to Novato Creek,

  2. the Petaluma Marshes extending from the mouth of the Petaluma River north to just south of the City of Petaluma on both sides of the Petaluma River,

  3. the south Napa Marshes extending from Sonoma Creek to the Napa River and bounded to the north by Napa Slough, South Slough, and Dutchman Slough,

  4. the Napa River wetlands including Coon Island, Fagan Slough wetlands, and the lands on the west side of the Napa River south of the Newport North development, and

  5. the Point Pinole wetlands extending from Wilson Point southwest around Pinole Point to Point San Pablo.

After discussions with several of the other focus teams, particularly the Other Birds team and the Shorebirds and Waterfowl team, we modified a portion of one of the areas the south Napa marshes, to preserve specific parcels with high existing values for several bird species. Pond 1, Pond 1A, and the West End Club originally proposed for restoration to tidal action are now recommended for preservation. The new description for the Napa marshes now includes the existing marshes south of Highway 37 between Sonoma Creek and the Napa River as well as the Cullinan Ranch and Guadalcanal Village north of Highway 37. In addition Pond 3 (Knight Island), Pond 2A (south half of Pond #2), and Pond 4 (the south half of Russ Island) are now included with these wetlands. The result of this modification is that the south Napa wetlands and the Napa River wetlands are connected and are combined into one large tidal wetlands complex, leaving four, not five distinct areas.

The Hamilton/Bel Marin Keys wetlands currently support good pickleweed marsh outboard of the levees at the south end of Hamilton Army Air Base (AAB) property and the Silvera and St Vincent properties. These marshes are valuable and must be preserved. To insure the long-term viability of salt marsh harvest mice in Marin County, however, it will be necessary to expand this wetland complex and provide for areas of upland refugial habitat. The Hamilton AAB site is being considered for restoration to tidal action as part of the base closure/clean up process. The western edge of Hamilton should be restored to an upland buffer that gradually changes from tidal marsh to the existing inboard levee. The adjacent State owned antenna field could be included as part of the Hamilton AAB tidal restoration. There is currently little or no marsh outboard of the levee along most of the Bel Marin Keys property. Existing mouse populations around the mouth of Novato Creek are isolated from populations immediately to the south. The restoration of at least the eastern portion of the Bel Marin Keys site would provide continuous tidal marsh extending from Las Gallinas Creek to Novato Creek. Upland buffer should also be provided along the western edge of the Bel Marin Keys parcel as a necessary component of the restoration.

The marshes along the west side of the Petaluma River north of San Antonio Creek are the largest block of tidal salt marsh remaining around San Francisco Bay. Although these marshes have been ditched for mosquito abatement purposes and levies constructed along portions of the eastern edge for an unrealized filling of the marsh, this wetland complex remains the least disturbed tidal marsh in the North Bay. The restoration of tidal wetlands south of San Antonio Creek to the mouth of the Petaluma River is considered vital to the future health of the salt marsh harvest mouse populations in this area and important to the vitality of the marsh system as a whole. We recommend restoration of significant amounts of former tidal marsh on the east side of the Petaluma River to create a block of tidal marsh large enough to provide for genetic variability and population stability of salt marsh harvest mouse populations in this area.

The lands along the east side of the Petaluma River should provide a transition from tidal wetlands into uplands resulting in needed refugial habitat. It is not possible to create this upland habitat on the west side due to the existing railroad line at the western boundary of the existing wetlands. Another component of this marsh complex extends from the mouth of the Petaluma River to Tolay Creek. Portions of this area are already tidal marsh or are being restored to tidal action (Sonoma Baylands and Tolay Creek south of Highway 37). However the most benefit will be realized when the steep levies that presently separate the tidal marsh from adjacent lands are removed and a buffer established that gently slopes from salt marsh to upland.

The Napa marshes include the existing tidal marshes south of Highway 37 between Sonoma Creek and the Napa River. Portions of these marshes around Mare Island support some of the highest densities of salt marsh harvest mice in the entire North Bay. For this reason some of the former military lands of Mare Island are proposed for restoration to tidal action. The remainder of the Napa marshes wetlands are on the west side of the Napa River and extend upriver to just south of the City of Napa. Much of this acreage is former Cargill Salt Company salt ponds presently owned by the California Department of Fish and Game (CDFG). CDFG currently has plans to restore a number of the salt ponds to tidal action as does the US Fish and Wildlife Service on the Cullinan Ranch which it owns. The restoration of the parcels along the west side of the Napa River will provide a solid tidal salt marsh block on the northeast side of the north bay and up the lower Napa River that should support healthy populations of salt marsh harvest mice independently of other populations.

The Point Pinole wetlands constitute the best opportunity to support a viable population of salt marsh harvest mice in the East Bay. This area is also extremely important because the San Pablo Creek marsh is the only locality for the endemic San Pablo vole. Restoration and enhancement of this area will protect this subspecies and should provide sufficient habitat for its continued survival. The possibility of restoring large tracts of tidal salt marsh in the East Bay is limited due to extensive fill and development. Although a number of small, healthy unconnected patches of wetlands can be found along the Contra Costa shoreline in the North Bay, we believe that they are too small and too isolated for long-term mouse viability. The MARI team recognizes that this area is considerably smaller than the other three recommended areas and may be too small to support target species without some maintenance efforts in the future. However, these wetlands represent the best opportunity to preserve/restore a block of tidal marsh with uplands on the east side of the Bay in this Region. In addition to the four major wetland complexes recommended in the North Bay there are a number of specific areas that our Focus Team believed merited special protections:

  1. The marshes near San Clemente Creek at Corte Madera and south of San Rafael Creek in Marin County are important because they support a small population of the southern sub-species of salt marsh harvest mouse. This is the only area where this sub-species is known to occur north of the San Mateo Bridge and is the northern most extent of the range of this sub-species.

  2. The Corte Madera marsh is also important because it serves as a harbor seal haul out and pupping site. This site has deteriorated over the past few years from shoreline erosion and would be greatly enhanced if wave action were reduced and the haul out site stabilized.

  3. There is a small area near Sears Point that supports a healthy population of red-legged frogs that warrants protection and enhancement.
  4. The slough channels throughout the marshes and salt ponds between Sonoma Creek and the Napa River provide habitat for river otter and the enhancement of adjacent marshes could benefit this species.

Central San Francisco Bay Region

The Central Bay Region is extends on the west side of the Bay from Point San Pedro (Marin Co.) in the north to Burlingame (San Mateo Co.) in the south. On the east side, it begins at Point San Pablo (Contra Costa Co.) and goes south to Mulford Landing, just north of the flood control channel in San Lorenzo (Alameda Co.). Thus the northern boundary coincides with the narrowest stretch of San Pablo Strait, while the southern boundary is an arbitrary line drawn about 4 1/2 miles north of the San Mateo Bridge. The Bay margins in this Region carry the highest human densities in the entire SF Bay system, and correspondingly sustain the greatest anthropogenic impacts.

Historically, the Central Bay Region had only 7% of the estimated acreage of tidal marsh in the Bay system, although it had 27% of the intertidal mudflats (EcoAtlas version 1.021). Proportionally, it has suffered greater losses in both of these habitat categories than has the Bay as a whole: 94% of its tidal marshes (82% in the entire Bay), and 71% of the mudflats (59% in the entire Bay) (EcoAtlas version 1.021). Those remaining habitat patches are small and widely scattered. A few hundred acres of tidal marsh pannes are estimated to have been present originally within the tidal marsh habitat. This represents 2.5 to 4.5% of the total estimated acreage of pannes in the Bay system (EcoAtlas version 1.50). Presently, no significant panne habitat remains in the Central Bay Region.

The habitats of greatest concern to the MARI team are the tidal marshes, adjacent uplands (including fresh water sites), and riparian corridors. In addition, salt (intertidal) pannes probably represented unique habitat for some terrestrial invertebrates. Because these critical habitats survive in the Central Bay only in small, isolated fragments, we have few site specific recommendations for this Region. Our general recommendations are:

  1. In general, the remaining wetland fragments are too small and isolated to support secure source populations for our target species.

  2. Surviving wetlands should be protected and where possible enhanced, because (a) they serve as important stepping stones for the movements of organisms within the Bay system; (b) such sites can at least temporarily support populations of the target species and hence contribute to overall metapopulation survival; (c) small populations can contribute to maintaining genetic variability within the Bay system and as refuges from unanticipated disasters in the source populations (disease, predation, pollution); (d) even small wetlands can serve as temporary feeding or resting sites for more mobile species (such as birds); and (e) Central Bay wetlands are important esthetic and educational resources.

  3. When opportunities arise, enhancement and enlargement of existing wetlands should be pursued. An example of such an unanticipated opportunity is the current 71.5 ac. restoration project in San Leandro Bay adjacent to Arrowhead Marsh (Martin Luther King, Jr. Regional Shoreline Wetlands Project). Significantly, this project will create two islands and an adjacent uplands buffer zone. The marsh-upland ecotone has all but vanished from the Bay Area, and yet is of critical importance to a number of our target species. Other feasible enhancements include the cleaning up of marshes (e.g., Emeryville Crescent), the provision of corridors to connect small existing wetlands (e.g., East Bay Shoreline Park in Richmond and Albany), and the restoration of creeks flowing into the Bay.

Site-specific recommendations:

  1. A small existing freshwater marsh in Millbrae along the west side of the San Francisco airport should be preserved and if possible enhanced for the benefit of the San Francisco garter snake and red-legged frog. Enhancements should include expansion of adjacent upland habitat.

  2. The Strawberry Spit area in Richardson Bay (Marin Co.) has been used as a haulout site for harbor seals, and this could be enhanced by reducing human disturbance.

  3. The Corte Madera marshes could be greatly increased in value if upland buffers were established on its periphery. It can also serve as a haul-out and pupping site for harbor seals.

  4. The San Rafael Bay marsh should be maintained as a source habitat for other wetlands, current or future, along the Marin Co. bay edge.

  5. The Castro Rocks near the Richmond-San Rafael Bridge are an important haul-out and pupping site for harbor seals, and should be protected.

  6. A small marsh (now in private ownership) at the end of the Tiburon Peninsula (Keil Pond, near Bluff Point) should be preserved and enhanced for the benefit of red-legged frogs.

  7. We support the development of tidal marshes in association with Crissy Field in San Francisco, and any other similar projects within the city.

  8. It would be highly desirable if the existing Arrowhead Marsh (Alameda Co.) could be connected to upland habitat while preferably maintaining its isolation from red fox and other predators.

South San Francisco Bay Region

We subdivide the South San Francisco Bay region into seven sectors starting from the northeast and swinging around to the northwest aspect of the South Bay: (1) (the Landings Sector) that includes the marshes from Hwy. 92, i.e. the San Mateo Bridge hwy. , north to the San Leandro Marina or Mulford Landing and named after Johnson, Hayward and Robert's Landings along its edge, (2) (Baumberg/Alameda Flood Control Sector) the area between Hwy. 92 and Coyote Hills Slough, the second of the large flood control channels south of Hwy. 92, (3) (Coyote Hills Sector) the area between Coyote Creek Slough and Hwy. 84, the Dumbarton Bridge road, (4) (Refuge Central Sector) the area between Hwy. 84 and Mowry Slough, (5) (Alviso Sector) the area between Mowry Slough and Stevens Creek just west of Moffett Field, (6) (Palo Alto Sector) the area from Steven's Creek to Hwy. 84, and finally (7) the (Bair/Greco Islands Sector) the area from Hwy. 84 to Hwy. 92. A simplified table follows:

There are some important and fairly large marshes still present in the South Bay. They include the string of marshes that make up the Landing Sector, the Baumberg Tract within Baumberg/Alameda Flood Control Sector, the Dumbarton, Mowry and Calaveras marshes in Refuge Central Sector, the Greco and Bair Islands in Bair/Greco Islands Sector, and to some degree the Palo Alto Educational Center Marsh in the Palo Alto Sector. Many of the marshes within the Alviso Sector, with the exception of the Calaveras Point Marsh, have been or are being converted rapidly from saline to brackish vegetation that does not support salt marsh harvest mice and to some extent either salt marsh wandering shrews or California voles. The loss of much of the Alviso Sector has resulted not only in the loss of many salt marshes but has produced a major barrier to gene flow between the populations of mice, shrews and voles on the east and west sides of the southern end of the South San Francisco Bay (hereafter we will call it the South Bay). Indications are that parts of the large Calaveras Point Marsh are also beginning to become brackish; its loss would be a tragedy because it appears to contain the largest single population of the southern subspecies of the salt marsh harvest mouse.

Aside from the few remaining large blocks, most of the tidal salt marshes of the South Bay are

Geographic location Name of Sector
North of Hwy. 92, East side Landings
Hwy. 92 to Coyote Hills Slough Baumberg/Alameda Flood Control
Coyote Hills Slough to Hwy. 84 Coyote Hills
Hwy. 84 to Mowry Slough Refuge Central
Mowry Sl. to Stevens Creek Alviso
Stevens Creek to Hwy. 84 Palo Alto
Hwy. 84 to Hwy. 92, West side Bair/Greco Islands


narrow, strip marshes (many two meters wide or less) with little to no upper edge of peripheral halophytes (the escape cover salt marsh harvest mice need and without which such marshes often lose their harvest mice). The poor quality of most of the salt marshes in the South Bay makes the pre-existing large marshes listed previously extremely important to the long term survival of the southern subspecies of the salt marsh harvest mouse especially since any long term conversions of salt ponds to tidal salt marshes may take five to twenty five years or more.

Recommendations without major conversions of salt ponds.

Here are our recommendations for marsh enhancement before the many salt ponds we have identified are returned to tidal action.

  1. Connect the large, protected tidal or muted tidal marshes of the Landings Sector with corridors of at least 100 yards wide and composed of halophytic (salt tolerant) vegetation appropriate for the salt marsh harvest mouse and the shrews. Protect the upper edges of the present marshes as well as corridors, if possible, with areas of marshy, ruderal and/or grassland vegetation at least 100 yards deep to act as buffer zones for them. We think that corridors need "edges" as much if not more than larger marshes.

  2. Expand the areas of salt marsh within the Baumberg area within the Baumberg/Alameda Flood Control Sector by at least twice the size that is presently under restoration.

  3. Enhance the Alameda Flood Control "marshes" just north of Coyote Hills Slough and running from the Bay towards the south Union City area and then south and west towards the hill just north of the Slough and the Coyote Hills to the south of that hill and manage them for year round use by small rodents (not just winter flood control use). These marshes need better connections between units and the total area of salt marsh needs to be expanded at least by a third. We have no short-term recommendations for the salt ponds of the Coyote Hills Sector. Long range plans involve opening part to most of them to tidal action.

  4. The Dumbarton Point marsh and the marshes along Newark Slough west of the refuge headquarters hill in the Refuge Central Sector need expansion and increased protection. Marshes along Newark Slough east of the hill, i.e. south of Thorton Ave. and west of Newark (the Jarvis Landing Area), need to be both expanded and protected from urban build out. Part of the eastern end of this area is within the City of Newark. Enhancement includes better water management, adding a 100 yard buffer of marsh or ruderal or grassland vegetation and conversion of adjacent salt ponds to tidal action and connecting them to existing units wherever possible.

  5. The Calaveras Point Marsh within the Alviso Sector needs to be expanded by opening the two outer salt ponds between Mowry Slough and Coyote Creek to tidal action. The Calaveras Pt. Marsh extending eastward along Coyote Creek is extremely important to the harvest mouse and the Mowry Slough marshes are important to the mouse, shrew, vole and harbor seal.

  6. The "Triangle" Marsh north of Alviso and west of the railroad tracks and bordering Coyote Creek within the Alviso Sector has been virtually lost to the harvest mice and shrews by the effects of brackish waters. The only salvation of this former highly productive salt marsh is saltier water. This area has almost completely turned into brackish vegetation because of non-saline sewage waters entering the bay from the San Jose-Santa Clara Water Treatment Control Plant. Many of the marshes of the Alviso Area (Albrae, Mud Slough, Upper Coyote Creek, Artesian Slough) are similarly dependent on increased salinities for reconversion back to saline marshes. They also need to be expanded from their present narrow, strip-like character to be of much value to mammals; however to increase the width of these strip marshes will require the conversion of some to many adjacent salt ponds as there is no intermediate step possible in the most southern South Bay.

  7. The New Chicago Marsh within the refuge in the Alviso Sector has some water management but the pumps used for that management need improvement and additional funding is needed for increased staff time for management by San Francisco Bay National Wildlife Refuge Complex biologists. The refuge complex needs more biologists and better funding from the USFWS in general to manage the enormous variety and size of their holdings, especially if many to most of the salt ponds in the South Bay are eventually converted to tidal action.

  8. The marshes between Charleston Slough to Cooley Landing in the Palo Alto Sector, including the Palo Alto Education Center Marsh, need more upland buffers, better protection from illegal entry, more alien predator management and better marsh corridors or connections between present marshes. Again the 100 yard minimum rule and appropriate vegetation rule applies to both buffers and upper edges. The Palo Alto marsh continues to change in vegetation (for the worse) and the upland edge of the marsh is very abrupt and needs modification.

  9. Bair Island (Bair/Greco Islands Sector) needs to have more marsh habitat now that it looks like it will be protected.

  10. The strip marsh along Ravenswood Pt. (Bair/Greco Islands Sector) need to be expanded to the south by opening the salt ponds adjacent to it to tidal action.

  11. Greco Island (Bair/Greco Islands Sector) needs better protection by opening up areas south of Westpoint Slough to tidal action.

Recommendations for major conversions of salt ponds to tidal action

. We think it is important preserve, expand and improve the existing marshes previously identified wherever and however possible. But to insure the long-term survival of the southern subspecies of the mouse and probably the salt marsh wandering shrew and California vole in the South Bay, as well as many species of birds, other vertebrates and invertebrates, we recommend that most of the salt ponds of the South San Francisco Bay be opened to tidal action (see map). We assume commercial salt production will cease some day in the South Bay, either when the salt company stops making salt and sells its assets or it is bought out as mitigation for other modifications within the Bay. Unless the salinity of the waters of the southern part of the South Bay is increased (i.e. be returned more towards historic salinity), marsh development in many of these areas will result in brackish rather than saline marshes. There are plans to open the Knapp Property, the bayward "thumb" of the former salt ponds between Alviso and Guadalupe Sloughs in the Alviso Sector, to tidal action. While it will be an important conversion, it will do little by itself for the endangered and threatened small mammals of the southern end of the South San Francisco Bay.

The very large tidal salt marsh complexes that will be created if most of the ponds are opened to tidal action are expected to be multiple-use in that levees and saline pannes can be left within them to support resting and feeding sites for various species of birds. Small ponds or areas of open water can be included so long as the salinity levels of such areas of water do not have to be maintained. The large marshes can have complex shapes and surround or otherwise be integrated with other types of saline plant or water environments. What is paramount to save the various species of mice, as well as the California Clapper Rail, is that the new complexes be tidal salt marshes, not brackish marshes. The marshes need to be very large ones (1,000 acres or more) with extensive and wide margins of both peripheral halophytes and grassland buffers of at least 100 yards but better yet more than 200 yards in width. And where corridors are needed to connect isolated marshes to increase the overall size of the connected marshes (such as are needed between the marshes of the Landing Sector), the corridors should be wide (at least 100 yards, be composed of appropriate salt marsh vegetation, have gently-sloping edges of approximately 100 yards and be at least partially protected from intrusion by humans and non-native predators such as the red fox and be managed to control such predators on a continual and perpetual basis. We recommend large corridors be established or maintained between large marshes but that corridors much less than 100m be established or maintained between small marshes of 1 or 2 to 10 acres. The wider the corridor and the more appropriate the vegetation, the more likely the corridor will facilitate movement between marshes, but in the short run just connecting small marshes is a very important first step. We recommend smaller connections but think that the recovery effort should proceed beyond them as more land for both corridors and the marshes connect become available.

Studies needed prior to major salt pond conversions.

We think it is imperative that a series of studies be carried out before many of the large salt ponds, especially those in the most southerly and most subsided portion of the South Bay are breached and returned to tidal action. These studies need to identify such things as how long it will take for restoration to occur in various parts of the South Bay, how the ponds and levees can be engineered to provide the greatest benefit to the most species and at the lowest maintenance costs. We need to determine whether mud flats and ponds will be created in ways to help support various species of waterfowl and wading birds as well as other vertebrate species, many of which are dependent on and often endemic to the tidal marshes of San Francisco Bay.

More money needs to be provided to the California Department of Fish and Game to allow them to actively manage the salt ponds and newly developing marshes of the San Pablo Bay. The CDFG can provide valuable information about marsh restoration around the entire Bay if they can proactively manage those marshes. Several other marshes are being restored in the South San Francisco Bay, i.e. parts of the Baumberg Marsh on the east side of the South Bay and several marshes between Charleston Slough and Hwy 84 on the west side of South Bay. None of these "experiments" are in the deeply subsided southern tip of the Bay. Marsh restoration in this latter area needs to be modeled by physical and biological scientists working (the words "alike together" have been deleted) together.

The South San Francisco Bay was once filled with marshes and mud flats as well as smaller salt pannes and tidal ponds. We think it should be returned to that general condition but not before studies are done to model the effects of converting salt ponds to tidal action, especially in the most subsided portions of the Bay. Such studies need to be carried out soon. And, increased funding sources need to be identified as the management of the South Bay will become more costly in the future no matter what scenario takes place.

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