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Compilation of Focus Teams and Hydrogeomorphic Advisory Team Recommendations: Fish and Aquatic Invertebrate Focus Team Recommendations

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Contents

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

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June 1998

Notice

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.

Fish and Aquatic Invertebrate Focus Team Recommendations

This paper summarizes the Fish Focus Team's habitat recommendations and restoration principles. Information is presented for each of the key habitats that fish utilize. For additional information regarding the fishes that occur in the baylands and adjacent waters of San Francisco Bay, please refer to the individual species narratives that will be compiled in the Goals Project's Focus Team Species/Community Narrative Report

Shallow Bay or Strait (unvegetated)

Recommendations:

• Avoid any net loss of this habitat through solid bay fill.

• Restore shallow subtidal habitat in Suisun Bay (benefits Delta smelt, splittail, steelhead trout, etc.).

• Restoration of shallow subtidal habitat is encouraged in previously maintained and/or created artificial deepwater areas (e.g., former navigation channels or berthing areas).

• Maintain or create linkages to tidal marsh to maximize value for fishes

Restoration Principles: (none advanced)

Benefits:

• In addition to those identified above, see Table 1.

High/Mid-Tidal Marsh

Recommendations:

• Preserve this habitat throughout the region, particularly in central San Francisco Bay where the decline has been the most dramatic.

• Maximize restoration of this habitat throughout the remaining subregions (i.e., Suisun Bay, San Pablo Bay, and South San Francisco Bay), particularly in historic diked baylands where the best opportunities appear to exist.

Restoration Principles:

• Create large, continuous patches of high/mid-tidal marsh which will support a wide variety of channel orders (e.g., 3rd and 4th order for maximum edge), within an appropriate range of salinity, seasonality of water flow, and other features of the natural hydrograph. This will particularly benefit marsh resident species (e.g., longjaw mudsucker) and juveniles of seasonal residents (e.g., splittail, chinook salmon, etc.).

• There should be significant linkages to low tidal marsh and adjacent upland habitats to maximize functional values for fish, invertebrates, and all marsh species, as well as promote a self-sustaining capability.

• There is a need for dead-end sloughs in Suisun Bay, particularly those with emergent and submerged vegetation. Beneficiaries include, splittail, Delta smelt, tule perch, and opossum shrimp.
• There should be potential for freshwater streams to connect within the marsh during high flow years this promotes species diversity and genetic exchange.

• Encourage the presence and maintenance of high tidal marsh pannes for the benefit of certain invertebrates (e.g., California horn snail).

Benefits:

• In addition to those identified above, see Table 2.

Low Tidal Marsh

Recommendations:

• We should preserve all existing low tidal marsh areas throughout all four subregions of the Estuary.

• Restoration efforts for low tidal marsh should be focused in areas of historical distribution or as transition zones in conjunction with high tidal marsh development plans.

Restoration Principles:

• Restore large, continuous patches (> 200 acres) of low tidal marsh in areas, particularly within the Suisun Bay subregion, where suitable land elevations exist near important rearing sites (i.e., shallow water areas of Suisun, Honker, and Grizzly Bays) for juvenile fishes (e.g., Delta smelt, chinook salmon, etc.). Tidal marshes adjacent to these open bays, especially the northern shore, are even more valuable to chinook salmon and Delta smelt than are dead end sloughs in the inner marsh.

• Low tidal marshes should occur at the mouths of all small streams, creeks, etc. entering San Francisco Bay. Marsh benefits include foraging and smolting and protective habitat for salmonid juveniles and adults.
• Linkages to high/mid-tidal marsh and intertidal flat should be maintained and/or created.

• Low tidal marshes should have an array of channel types, especially some within a short distance of the bay or strait which are not dewatered at low tide. Diverse and abundant native fish populations are found in these types of channels as they probably function as refugia from major predators.

• Tidal marshes should be exposed to a full tidal range and not controlled by tide gates or muted with a man-made or maintained structures. By controlling tidal range or amplitude, fish movements are limited, temperatures may increase, and some water quality parameters may decline. Former tidal marshes which have subsided and are subsequently opened to controlled tidal action may not develop to a more "natural marsh", including deeper channels which function as refuge from predators. Refuge is an important issue in areas which are maintained at relatively shallow depths, as predation, especially by birds, may be high in such areas.

• No actions should be taken that interfere with physical processes which may cause a transition to high/mid-tidal marsh.

• Restoration management plans for low tidal marsh should include eradication of deleterious invasive plant species (e.g., Spartina alterniflora).

Benefits:

• In addition to those identified above, see Table 3.

Intertidal Flat

Recommendations:

• Protect all intertidal flats at current levels and locations in central San Francisco Bay where increases from historical levels are relatively low and, at a minimum, protect at historical levels in the other three subregions.

• We do not recommend restoration efforts for this habitat except as part of larger projects where it is a necessary transition zone between low tidal marsh and shallow bay (i.e., shallow subtidal), or as compensatory mitigation for direct losses of intertidal flat.

Restoration Principles:

• Since intertidal mudflats are an integral part of the channel system within tidal marshes, habitat characteristics advanced previously for those habitats (e.g., channel complexity) should be adhered to.

• Intertidal mudflat should be protected from low-growing eastern cordgrass, Spartina alterniflora.

Benefits:

• In addition to those identified above, see Table 4.

Salt Ponds

Recommendations:

• Relative to mature tidal marshes, salt ponds provide minimal habitat value to fishes and aquatic invertebrates; therefore, where possible, they should be converted to tidal marsh and other aquatic habitats by opening them to full tidal action. Depending upon the location of the restored ponds, different species and functions would be supported.

Restoration Principles:

• See tidal marsh and intertidal flats as described above.

Benefits:

• Same as above.

Eelgrass

Recommendations:

• Due to its unusually high value to fish and wildlife resources, all existing eelgrass beds within the region need to be identified and vigorously preserved.

• Eelgrass restoration efforts should be located within South San Francisco Bay, Central San Francisco Bay, and San Pablo Bay as a result of the apparent influence of fresh water on its distribution.

Restoration Principles:

• Restoration should take place only in those areas where key water quality features (e.g., water clarity, well-oxygenated sediments, etc.) indicate a high likelihood of success.

• Enhancement of existing eelgrass beds should be limited to the revegetation of unvegetated areas within the bed's margins.

Benefits:

• See Table 5.

Tidal Rivers, Creeks, and Streams

Recommendations:

• Protect what we have region-wide.
• To extent feasible, restore to the historical levels of dead-end sloughs.

Restoration Principles: (None advanced).

Benefits: (None advanced).

 

Table 1: Functional Support for Target Species by Shallow Bay and Strait Habitat

Species	Suisun Bay	San Pablo Bay	Central S.F. Bay	South S.F. Bay
leopard shark			spawning & forage	spawning & forage
bat ray				forage & protection
white sturgeon	forage & movement	forage & movement	forage	forage
Pac. herring		forage	spawning, forage, & movement	spawning, forage, & movement
splittail	forage & protection	forage & protection
Delta smelt	forage
longfin smelt	forage	forage
no. anchovy			spawning & forage	spawning & forage
steelhead trout	forage & movement	forage & movement	forage & movement	forage & movement
chinook salmon	forage & movement	forage & movement	forage & movement
topsmelt		forage		forage
jacksmelt		forage	forage	forage
plainfin midshipman			spawning, forage, movement, & protection
brown rockfish			forage & protection
Pac. staghorn sculpin		forage & protection	forage & protection	forage & protection
striped bass	forage	forage	forage	forage
white croaker			spawning & forage
shiner perch		forage	forage	forage
arrow goby		spawning, forage, & protection		spawning, forage, & protection
bay goby			forage & protection
Ca. halibut			forage & protection
starry flounder	forage & protection	forage & protection	forage & protection
opossum shrimp	forage	forage
softshell clam		spawning, forage, & protection	spawning, forage, & protection	spawning, forage, & protection
amphipods	spawning, forage, & protection	spawning, forage, & protection	spawning, forage, & protection	spawning, forage, & protection
Ca. bay shrimp	forage & protection	forage & protection	spawning, forage & protection	forage & protection
blacktail bay shrimp			spawning, forage, & protection
Dungeness crab		forage, movement, & protection	forage, movement, & protection	forage, movement, & protection
rock crabs			spawning, forage, & protection
mud crab		spawning & forage	spawning & forage	spawning & forage

 

Table 2: Functional Support for Target Species by High/Mid-Tidal Marsh Habitat

Species	Suisun Bay	SanPablo Bay	Central S.F. Bay	South S.F. Bay
splittail	forage & protection	forage & protection
chinook salmon	forage & protection	forage & protection	forage & protection	forage & protection
rainwater killifish	spawning, forage, movement, & protection			spawning, foraging, movement, & protection
topsmelt				forage
threespine stickleback	spawning, forage, & protection	spawning, forage, & protection		spawning, forage, & protection
prickly sculpin	forage & protection	forage & protection	forage & protection	forage & protection
striped bass				forage
tule perch	spawning, forage, & protection	spawning, forage, & protection
longjaw mudsucker		spawning, forage, & protection		spawning, forage, & protection
Assiminea californica	spawning & forage	spawning & forage	spawning & forage	spawning & forage
California horn snail			spawning & forage	spawning & forage
ribbed mussel				spawning, forage, & protection
amphipods	spawning, forage, & protection	spawning, forage, & protection	spawning, forage, & protection	spawning, forage, & protection
mud crab		forage & protection	forage & protection	forage & protection

 

Table 3: Functional Support for Target Species by Low Tidal Marsh Habitat

Species	Suisun Bay	San Pablo Bay	Central S.F. Bay	South S.F. Bay
bat ray				forage & protection
white sturgeon		forage & protection	forage & protection	forage & protection
splittail	forage & protection	forage & protection
chinook salmon	forage & protection	forage & protection	forage & protection	forage & protection
rainwater killifish				spawning, foraging, movement, & protection
topsmelt				forage
threespine stickleback	spawning, forage, & protection	spawning, forage, & protection	spawning, forage, & protection	spawning, forage, & protection
prickly sculpin	forage	forage	forage	forage
Pac. staghorn sculpin		forage	forage	forage
striped bass	forage	forage	forage	forage
tule perch	spawning, forage, & protection	spawning, forage, & protection
arrow goby		forage & protection		forage & protection
longjaw mudsucker		spawning, forage, & protection		spawning, forage, & protection
starry flounder	forage & protection	forage & protection	forage & protection
Ca. horn snail			spawning & forage	spawning & forage
opossum shrimp	forage
amphipods	spawning, forage, & protection	spawning, forage, & protection	spawning, forage, & protection	spawning, forage, & protection
Ca. bay shrimp	forage & protection	forage & protection	forage & protection	forage & protection
Dungeness crab		forage	forage	forage
mud crab		spawning & forage	spawning & forage	spawning & forage

 

Table 4: Functional Support for Target Species by Intertidal Flat (Mud and Sand) Habitat

Species	Suisun Bay	San Pablo Bay	Central S.F. Bay	South S.F. Bay
leopard shark			forage	forage
bat ray				forage & protection
splittail	forage & protection	forage & protection
chinook salmon	forage & movement	forage & movement	forage & movement
jacksmelt		forage	forage	forage
plainfin midshipman			spawning, forage, movement, & protection
Pac. staghorn sculpin		spawning & forage	spawning & forage	spawning & forage
striped bass	forage	forage	forage	forage
white croaker			forage
shiner perch		forage	forage	forage
arrow goby		spawning, forage, & protection		spawning, forage, & protection
longjaw mudsucker		spawning, forage, & protection		spawning, forage, & protection
Ca. halibut		forage & protection	forage & protection	forage & protection
starry flounder	forage & protection	forage & protection	forage & protection
Ca. horn snail			spawning & forage	spawning & forage
softshell clam		spawning, forage, & protection	spawning, forage, & protection	spawning, forage, & protection
amphipods	spawning, forage, & protection	spawning, forage, & protection	spawning, forage, & protection	spawning, forage, & protection
Ca. bay shrimp	forage & protection	forage & protection	forage & protection	forage & protection
Dungeness crab		forage	forage	forage
mud crab		spawning & forage	spawning & forage	spawning & forage

 

Table 5: Functional Support for Target Species by Eelgrass Habitat

Species	Suisun Bay	San Pablo Bay	Central S.F. Bay	South S.F. Bay
white sturgeon		forage	forage	forage
Pac. herring		forage	spawning & forage	spawning & forage
chinook salmon		forage	forage	forage
topsmelt				spawning & forage
jacksmelt		spawning & forage	spawning & forage	spawning & forage
Pac. staghorn sculpin		forage & protection	forage & protection	forage & protection
shiner perch		spawning & forage	spawning & forage	spawning & forage
amphipods		spawning, forage, & protection	spawning, forage, & protection	spawning, forage, & protection
Ca. bay shrimp		forage & protection	forage & protection	forage & protection
mud crab		spawning & forage	spawning & forage	spawning & forage