biological foundations of the san francisco bay joint...

US COASTAL SURVEY, 1857

Biological Foundations of the San Francisco Bay Joint Venture

Biological Foundations of the San Francisco Bay Joint Venture

Transforming the Landscape

Before the mid-1800s, the San Francisco Bay wasringed by roughly 190,000 acres of tidal marshes,

50,000 acres of tidal flats, 85,000 acres of seasonalwetlands and associated uplands (including vernalpools), and over 69,000 acres of riparian habitat, asillustrated in Figure 2-1, (Historical View of SanFrancisco Bay, circa 1770–1820). The San FranciscoBay and its adjoining watersheds was one of therichest and most diverse estuaries on the WestCoast; it supported populations of fish and wildlifethat today seem unimaginable. Early reports of theBay Area describe vast expanses of wetlands inhab-ited by millions of waterfowl, schools of salmon sodense that they choked the mile-wide CarquinezStrait, and plentiful numbers of grizzly bears andother big game animals.

Since the late 1800s, the growth of the humanpopulation has effected traumatic changes to thenatural landscape of the Bay Area. Large tracts of tidal marshes have been filled for urban develop-ment or federal and state projects, or diked for saltproduction or agriculture. Today, only 40,000 acresof tidal marsh remain, as shown in Figure 2-2, (Modern View of San Francisco Bay, circa 1998).Much of what remains has been degraded, and lessthan three percent of original wetland acreage is inrelatively pristine condition (State of the EstuaryReport 1992–1997). Development pressures have

destroyed or significantly altered over 80 percent ofthe tidal marshes and 40 percent of the mudflatsthat once rimmed two-thirds of the Bay’s shores.During this same period, riparian areas, seasonalwetlands, vernal pools, native grasslands, andcoastal scrub have all suffered similar, if not greater,losses due to development pressures.

The destruction or alteration of wetlands isnot limited to the forces of urbanization. Pollution,sedimentation, and water diversion have degradedthe health of the surviving wetlands. Historic influ-ences such as hydraulic mining also play a role, andtheir impacts can be persistent over time. The GoldRush-era mining of the mid-1800s sent enormoussediment loads into the Bay, causing changes inhabitat type and location, particularly of mudflats inthe North Bay. What remains of the Bay ecosystemis further stressed and modified by the impacts offreshwater diversions for urban uses around theBay, and agricultural and urban uses in the CentralValley and southern California. Up to 70 percent ofthe freshwater flows that would naturally enter theBay through the San Joaquin and Sacramento RiverSystems is now diverted. This has increased the netsalinity of the Bay with a consequent alteration ofthe plant and animal species residing in many wet-land communities. Local land uses have playeddirect and indirect roles in damaging wetlands: thefootprint of new buildings still displaces them; sedi-ment loads and erosion caused by developmentdegrade them. Stormwaters contaminated by auto-

2

8 Restoring the Estuary

Figure 2-1 Historical View of San Francisco Bay (circa 1770–1820)

Omiomi

Habasto

Huimen

Yelamu

Urebure

Ssalson

Lamchin

Puichon

Tamien"Santa Ysabel"

Alson

Tuibun

Yrgin

Jalquin

Huchiun

Huchiun-Aguasto Chupcan

Ompin

Malaca

Suisun

Carquin

Napa

Alaguali

Chocoime

Olompali

Petaluma

Deep Bay/Channel (>18 feet)

Shallow Bay/Channel (<18 feet)

Tidal Flat

Tidal Marsh

Tribal regions courtesy of Randall Milliken.

SCALE 1:450,000

0 4 8 12 16 Kilometers

0 2 4 6 8 10 12 Miles

Bay Area EcoAtlas ©1999 San Francisco Estuary Institute

Chapter 2—Biological Foundations of the San Francisco Bay Joint Venture 9

Figure 2-2Modern View of San Francisco Bay (circa 1998)

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Tidal Marsh

Diked Bayland

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SCALE 1:450,000

Bay Area EcoAtlas Version 1.50 ©1999 San Francisco Estuary Institute

Napa

Petaluma

Novato

San Rafael

Fairfield

Concord

Richmond

Oakland

Hayward

Fremont

Redwood City

San Mateo

San Francisco

San Jose

Vallejo

SonomaBaylands

Hamilton FieldMare Island

San Pablo Bay

Sacramento–San JoaquinRivers Confluence

Suisun Bay

Pacific Ocean

motive metals, pesticides from lawns, and high bac-terial counts continue to stress wetlands and pollutethe Bay.

Such drastic impacts to the Bay’s wetlandecosystem have put fish and wildlife populations, aswell as the ecological health of the Bay, at risk. Mostof the threatened and endangered species, andalmost all of the commercial and recreational fishspecies in San Francisco Bay depend on wetland andriparian habitat. Numerous adult and juvenile fishspecies that are dependent on tidal marshes, suchas Chinook salmon and delta smelt, have declineddramatically due to the loss of habitat. The loss of aonce-thriving fishing industry has also severelyimpacted the economies of numerous Bay cities.

Wetland losses and degradation would havebeen even more severe were it not for state and fed-eral regulations, active public and nonprofit acquisi-tion programs, and increased public awareness. Theprotection and enhancement of wetlands and ripari-an corridors has been given a tremendous boostwith the growth of watershed planning efforts thatbring diverse stakeholders together. Approximately16,300 acres of wetlands were permanently protect-ed in the Bay region between 1992 and 1999. In addi-tion, about 9,040 acres of degraded or former wet-land were restored and enhanced during this periodof time. (CCMP Workbook, 1996; SFBJV, 1999) Whilethese figures are encouraging, much of the reportedacreage is submerged tideland and represents afraction of the potential. There is a tremendousamount of protection, restoration, and enhancementwork remaining for wetlands, riparian areas, andassociated uplands.

The establishment of the SFBJV was hastenedby the growing realization among all parties thatimmediate action is needed. The costs of acquiring

and restoring the remaining wetlands of San Fran-cisco Bay have skyrocketed over the past decade,and are likely to continue to climb. Restorationwork, which often meant only breaching a dike, nowmay cost from $4,000 to $20,000 per acre, given theneed for extensive grading, planting, new dike con-struction, or temporary irrigation.

Wildlife of San Francisco Bay

Waterfowl Use of the San Francisco Bay Area

The San Francisco Bay Area is one of the most impor-tant coastal wintering and migrational areas forPacific Flyway waterfowl populations. Significantnumbers of the Pacific Flyway scaup (70%), scoter(60%), canvasback (42%), and bufflehead (38%) werelocated in the San Francisco Bay/Delta. According to1998 California Fish and Wildlife surveys, SanFrancisco Bay held the majority of California’s 1999wintering scaup (85%), scoter (89%), and canvas-back (70%) populations. More than 56 percent of theState’s 1999 wintering diving ducks were located inthe San Francisco Bay proper, which includes the saltponds and wetlands adjacent to the North and SouthBays. Although the San Francisco Bay is most recog-nized for its importance to diving ducks, large num-bers of dabbling ducks like pintail (23,500) andwigeon (14,000) were observed during the 1999 mid-winter waterfowl survey. For a more detailed analy-sis of winter waterfowl surveys for the San FranciscoBay Area, see Appendix F.

Regionally, the greatest variation observed in waterfowl numbers between years and seasons


Hydraulic mining in the Sierra foothills during the Gold Rushsent vast amounts of sediment downstream and into SanFrancisco Bay. COURTESY OF BANCROFT LIBRARY, UC BERKELEY

Dredging channels and levees have dramatically altered theface of the Estuary and armored its margins.COURTESY OF BANCROFT LIBRARY, UC BERKELEY

was in Suisun Bay, followed by the North Bay andNorth Bay salt pond regions. Waterfowl use wasmost consistent in the Central and South Bays, with some variation in the South Bay salt pondregion. The greater range of waterfowl use of the

North Bay may be due to the variability of salinityand the presence of wetlands in the adjacent delta.San Pablo Bay and Suisun Bay are greatly influenced by outflows from the Sacramento and San JoaquinRivers.


The San Francisco Bay is a key wintering and stopover area along the Pacific Flyway. US FISH AND WILDLIFE SERVICE

Waterfowl production in the San Francisco BayArea is typically limited to small numbers of mal-lards, gadwalls, northern pintails, cinnamon teals,and ruddy ducks. Tidal marshes, diked wetlands,and seasonal wetlands are the primary habitats ofnesting waterfowl. In addition, Canada geese havenested in the area in recent years.

The San Francisco Bay is of particular impor-tance to the future of canvasback and other diving duck populations of the Pacific Flyway. San Francisco Bay wetlands can—if protected,restored, and enhanced—play a significant role in meeting NAWMP’s overall objective of providingdiverse habitats and spreading waterfowl popula-tions over large geographical areas.

Other Important Species in the San Francisco Bay Area

Wetlands and adjoining uplands in the San FranciscoBay Area provide habitat critical to the survival ofalmost 50 endangered and threatened species (26animal and 22 plant species) protected by the feder-al or State Endangered Species Acts. See Table 2-1for a complete list of federal and state protectedspecies found in and around the Estuary.

In addition to state and federally listed species,the Bay Area is home to 16 fish and wildlife speciesand 13 plant species associated with wetlands thatare candidate or proposed candidate species for fed-eral endangered or threatened status. Of the fish andwildlife species, 15 of 16 candidates are associated

with wetlands. Enhancementand restoration of wetlandsthroughout the region willbenefit the populations ofmost of these species.

The number of special-status species resident in orusing Bay wetlands demon-strates the crucial impor-tance of these areas, theirlevel of degradation, and theoverwhelming need to hastenrestoration efforts.

Shorebirds. Shorebirds areamong the most conspicuouswildlife of the North and Southbays. Thirty-eight species of wintering and migratoryshorebirds were found in the

Bay between 1988 and 1995 on surveys performed bythe Point Reyes Bird Observatory (PRBO). Totalnumbers of shorebirds on these surveys ranged from340,000–396,000 in the fall, 281,000–343,000 in thewinter, to 589,000–838,000 in the spring. Approxi-mately two-thirds of the migrating and winteringshorebirds occurred in the South Bay.

According to the United States ShorebirdConservation Plan, San Francisco Bay is used byhigher proportions of wintering and migratingshorebirds within the U.S. Pacific coast wetland sys-tem than any other coastal wetland. Depending onthe season, San Francisco Bay accounted for the fol-lowing percentages of shorebirds in the wetlands ofthe contiguous U.S. Pacific Coast on the PRBO sur-veys: black-bellied plover, 55–62%; semipalmatedplover, 40–52%; black-necked stilt, 58–90%;


Canvasbacks take flight on Suisun Marsh. CENTRAL VALLEY HABITAT JOINT VENTURE,1995

Black-necked stilts are among the many shorebirds that win-ter in the San Francisco Bay Estuary. MARK RAUZON

American avocet, 86–96%; greater yellowlegs,26–41%; willet, 57–69%; long-billed curlew, 45–65%;marbled godwit, 46–68%; red knot, 39–76%; westernsandpiper, 54–68%; least sandpiper, 39–73%; dunlin,24–38%; and dowitcher, 49–72%.

Tidal flats, salt ponds, diked seasonal wet-lands, grazed uplands and, to a limited extent, saltmarshes are the chief habitats of shorebirds at theSan Francisco Bay. Species making the heaviest use

of tidal flats include black-bellied plover, willet, long-billed curlew, marbled godwit, western sandpiper,least sandpiper, dunlin, and short-billed dowitcher.Species making heaviest use of salt ponds includesnowy plover, black-necked stilt, American avocet,northern phalarope, and Wilson’s phalarope. Blackoystercatchers nest on the rocky shores of someislands in the Bay. Snowy plover, federally listed as athreatened species, killdeer, black-necked stilt, and


Table 2-1Threatened and Endangered Species of the San Francisco Bay EstuaryPlant and animal species listed under the Federal and/or State Endangered Species Acts

Species (T=Threatened, E=Endangered) Scientific Name

MammalsSalt marsh harvest mouse (E) Reithrodontomys raviventrisSteller sea lion (T) Eumetopias jubatus

BirdsTule greater white-fronted goose (T) Anser albifrons gambelliCalifornia brown pelican (E) Pelecanus occidentalisWestern snowy plover (T) Charadrius alexandrinus nivosusCalifornia clapper rail (E) Rallus longirostris obsoletusCalifornia black rail (T) Laterallus jamaicensis corturniculusCalifornia least tern (E) Sterna antillarum browniAleutian Canada goose (T) Branta canadensis leucopareia

Amphibians and ReptilesSan Francisco garter snake (E) Thamnophis sirtalis tetrataeniaGiant garter snake (T) Thamnophis gigasCalifornia red-legged frog (T) Rana aurora draytonii

FishChinook salmon (E) Oncorhynchus tshawytschaCoho salmon (T) Oncorhynchus kisutchSteelhead (E) Oncorhynchus mykissSacramento splittail (T) Pogonichthys macrolepidotusTidewater goby (E) Eucyclogobius newberryiDelta smelt (T) Hypomesus transpacificus

InvertebratesBehren’s silverspot butterfly (E) Speyeria zerene behrensiiCalifornia freshwater shrimp (E) Syncaris pacificaConservancy fairy shrimp (E) Branchinecta conservatioMyrtle’s silverspot butterfly (E) Speyeria zerene myrtleaeCallippe silverspot butterfly (E) Speyeria callippe callippeDelta green ground beetle (T) Elaphrus viridisValley elderberry longhorn beetle (T) Desmocerus californicus dimorphusVernal pool fairy shrimp (T) Branchinecta lynchiVernal pool tadpole shrimp (E) Lepidurus packardi

PlantsSuisun thistle (E) Cirsium hydrophilum hydrophilumSoft bird’s-beak (E) Cordylanthus mollis mollisKenwood Marsh checkermallow (E) Sidalcea oregana valida

Source: Baylands Habitat Goals, (1999); Life on the Edge, (1995)

American avocet nest in the salt ponds. Killdeer,black-necked stilt, and American avocet also nest inthe managed diked marshes of Suisun Bay.

Because of the great shorebird numbers, theWestern Hemisphere Shorebird Reserve Networkhas classified San Francisco Bay as a site of “Hemi-spheric Importance” for shorebirds—the highestpossible ranking.

Marsh Birds, Gulls, and Terns. The San FranciscoBay Estuary provides nesting habitat for a variety ofmarsh birds including snowy egret, great egret,black-crowned night heron, great blue heron, andCalifornia clapper rail. In 1990, it was estimated that350 pairs of great egrets were breeding in the SanFrancisco Bay, along with 160 breeding pairs of greatblue herons.

California clapper rails, a Federally listedspecies currently found only in San Francisco Bay,are among the most inconspicuous wildlife of theNorth and South bays, but are a good indicator ofthe health of Bay wetlands. Clapper rails occur pri-marily in emergent salt and brackish tidal marsh-lands having intricate networks of slough channels,and vegetation dominated by pickleweed and Pacificcordgrass. The total population size is currentlyestimated at around 1,200. Clapper rails were for-merly more numerous and ranged more widely.

Numerous human-related factors over the past150 years have caused their decline. These includehunting in the late 1800s and, more recently, preda-tion by non-native predators and habitat loss.Presently, California clapper rail populations arerestricted to fragmented marshes that are small insize, and lack a significant transition zone to terres-trial habitat that would buffer them from nearbyurban and industrial development. Habitat goalscalling for the restoration of significant amounts oftidal salt marsh habitat in the Bay would immedi-ately and directly benefit clapper rails by allowingmovement of individuals between isolated popula-tions and recolonization of unutilized habitat.

An extensive variety of other “colonial nestingbirds” are common in the San Francisco BayEstuary. These include western gull, California gull,Forster’s tern, Caspian tern, and double-crested cor-morant.

Raptors. Marshes, tidal flats, and grasslands provideexcellent feeding habitat for the northern harrierand other raptors. Other wetland-associated raptorsinclude merlin, peregrine falcon, red-tailed hawk,short-eared owl, black-shouldered kite, and burrow-ing owl. The bald eagle is rare, but it nests nearreservoirs and lakes, and preys on waterfowl andcoots. Loss of habitat is an enormous threat to rap-tors in the Bay Area.

Other Marine Birds. Open waters, large lakes, andsalt ponds provide habitat for loons, pelicans, andgrebes. Grebes found in the study area are the pied-billed grebe, eared grebe, horned grebe, Clark’sgrebe, and western grebe. Large open-water habitatsof the Estuary such as bays, lagoons, salt ponds, anddiked habitats are fall and winter habitats forCalifornia brown and the American white pelicans.

Migratory Songbirds. Over 50 species of songbirdsmake use of the remnant riparian zones around theBay. Among them are flycatchers, sparrows, thrush-es, woodpeckers, warblers, vireos, and swallows.Salt, brackish, and freshwater marshes house thesalt marsh yellowthroat. Song sparrows utilize tidalsalt and brackish marshes, and the tricolored black-bird is a resident of freshwater wetlands. Thesebirds are also affected by habitat loss; the number oftricolored blackbirds has diminished by 89 percentsince the 1930s, and only 6,000 pairs of Suisun songsparrow remain in the Bay Area.


Least bittern SAN FRANCISCO BAY JOINT VENTURE

Mammals. The most abundant marine mammalassociated with wetlands and deepwater habitats ofthe Estuary is the harbor seal. This species usestidal salt marshes and mudflats for breeding andhauling out, and deepwater habitats for foraging.The sea lion is another important marine mammal ofthe San Francisco Bay, while elephant seals andhumpback whales are significant species of the SanFrancisco/San Mateo coast. Tidal marshes providehabitat for the Suisun shrew, salt marsh wanderingshrew, and salt marsh harvest mouse.

Amphibians and Reptiles. Inhabiting Delta chan-nels, small rivers, creeks, lakes, ponds, and season-al wetlands are a wide variety of amphibians andreptiles. Several federally and/or state listedspecies are among them, including the Californiatiger salamander and the California red-legged frog.Among listed reptiles dependent on riparian habi-tat is the San Francisco garter snake; other riparianresidents include the striped racer and the westernpond turtle.

Fish and Shellfish. Wetlands and deep waters ofthe study areas provide important habitat for awide variety of fish and shellfish. Salt marshes andshallow water areas provide habitat for larval,juvenile, and adult fishes and shellfish includingshiner perch, top smelt, staghorn sculpin, stripedbass, and bay shrimp. Intertidal and sub-tidalareas of the North Bay serve as important spawn-ing areas for Pacific herring. Important commercialand sport fishes that utilize deepwater habitats

include northern anchovy, starry flounder, stripedbass, king salmon, sturgeon, steelhead, and Ameri-can shad.

Benefits of Wetland Restoration and Enhancement

Wetlands and riparian areas in the Bay Area areimportant oases of life set against the backdrop ofthe arid west. However, the value of wetlands andriparian habitats extends beyond the animal andplant communities they support. And while these areprofoundly important, as the prior chapter suggests,there are a myriad of other supportive functions thatmagnify their significance. These complementaryvalues underscore the rationale and need for pro-tecting and restoring wetlands. Riparian and wetlandhabitats play key roles in maintaining both a healthyecosystem and an economically vibrant region.Among these vital “ecological services” are theircapacity to absorb or buffer floodwaters, cleansepollutants from runoff, reduce sediment loads inrunoff, recharge overdrawn groundwater supplies,and contribute to a community’s identity and recre-ational amenities. Wetlands offer a broad range ofnon-biological benefits that include:

• Reduced flood damage. Wetlands can not onlyserve as biofilters but can also slow down andsoak up water that runs off the land. This capaci-ty can lower the volume of floodwaters anddiminish flood heights, thereby reducing shore-line and stream bank erosion. Preserving naturalwetlands can reduce or eliminate the need forexpensive flood control structures.

• Economic values—Food and related industries.The vast majority of our nation’s fishing andshellfishing industries harvest wetland-depend-ent species. This catch is valued at $15 billion a


Dungeness crab (Cancer magister) JOHN INASE

Striped bass LEE ADAIR

year. The economic benefits of wetlands alsoextend to other forms of commercial harvest-ing—in the case of the South Bay, shell mining.The South Bay formerly had one of the nation’smost productive oyster beds, its harvest servingmuch of the West Coast.

• Water quality enhancement. Wetlands can helpimprove water quality by filtering nutrients, organ-ic particles, and sediment carried by runoff. Manychemicals—fertilizers, human and householdwastes, toxic compounds—are tied to sedimentsthat can be trapped in wetlands. Plants and biolog-ical processes in wetlands break down and con-vert these pollutants into less harmful substances.

• Increased groundwater availability. Wetlandscan absorb water during and after rainfall. Someof this precipitation percolates into the ground-water supply. Hence, wetlands often do the vitaljob of recharging groundwater by passively“banking” water for use at a later date.

• Recreation. Wetlands also contribute to the econ-omy through recreational activities such as fish-ing, hunting, and bird watching. It is estimatedthat the annual economic value of wetlands state-wide in California is between $6.3 and $22.9 billion

(Habitat Goals, page 31). The 1996 National Surveyof Fishing, Hunting, and Wildlife-AssociatedRecreation reported that 3.1 million adult Ameri-cans hunt migratory birds including geese,ducks, doves, and other game birds. Nationwideit is estimated that hunters spend about $1.3 bil-lion on travel, equipment, and other associatedexpenses.

• Aesthetic and scenic values. The natural beautyand solitude of wetland areas provide opportuni-ties for bird watching, wildlife photography,painting, hiking, and simply relaxing while appre-ciating the wonders of nature. Wetlands are a vitalpart of lives, providing a peaceful place to reflectwhile offering respite from everyday stresses.

• Education and research. Tidal, coastal, andinland wetlands of the Bay Area provide educa-tional opportunities for nature observation andscientific study.

• Historic and archaeological values. Some wet-lands are of archaeological interest. In the SanFrancisco Bay region Indian settlements wereoften located in coastal and inland wetlands,especially at the mouths of creeks. Estuaries wererich sources of fish and shellfish.

• Community identity and vitality. The presenceof wetlands in a city or town strengthens its senseof identity and place. Wetlands and creeks help togive positive and vivid definition to a community,offering tangible indicators of the “quality of life”values that are increasingly important to the res-idents of a growing metropolis, yet are degradedby the homogenizing effects of urban sprawl.Likewise, they help define the urban edges byproviding physical separators between towns.Collectively, they confer a natural character andpresence within an urban area. Wetlands areessential to the identity and vitality of the Bayregion and its continued desirability as a place tolive and work.

• Estuary support. Wetlands provide importantnutrients to near-shore waters from decomposingvegetation, which provides support for coastalfood webs.

Subregional Characteristics

As previously described, the SFBJV has divided itsgeographic scope into five subregions: Suisun, North


Family fishing at Marin Headlands DON COPPOCK

Bay, Central Bay, South Bay, and the San Francisco/San Mateo Coast (Figure 1-1). These subregions coin-cide with those used by the Habitat Goals Project,with a few exceptions. The fifth subregion is the SanFrancisco/San Mateo Coast.

The subregions vary greatly in their habitatcomposition. In general, the North Bay and SuisunSubregions have the greatest areas of tidal marshesand moist grasslands/vernal pools, together pos-sessing more than 70 percent of the region’s habitatsof these types. The South Bay contains the over-whelming majority of riparian willow groves, andabout 50 percent of the mudflats. Figure 2-3 summa-rizes the subregional distribution of the estuary’smajor habitat types.

The following section provides a geographicand ecological overview of each of these five sub-regions, focusing on characteristics and status oftheir habitats.

North Bay Subregion

The North Bay subregion consists of the submergedlands, wetlands, and uplands of San Pablo Bay. It isbounded to the east by the Carquinez Strait, whichconnects it to the Suisun subregion just upstream.Downstream it abuts the Central Bay subregion atPoint San Pedro. The boundary climbs to the ridge-line of the East Bay hills and follows the ridgeline of


Figure 2-3 Habitat Types by Subregion

SuisunNorth Bay

Central Bay

South Bay

100%

50

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ssla

nd

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al F

lat

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al M

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ow

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North Bay

Central Bay

South Bay

Source: Bay Area EcoAtlas Modern View ©1999 SFEI

the watersheds draining north to the CarquinezStrait (a line roughly parallel to and north of Highway24). Its major watercourses include the Napa River,Sonoma Creek, Petaluma River, Novato Creek, andGallinas Creek. This subregion includes all of SolanoCounty, and portions of Marin, Sonoma, Napa, andContra Costa Counties.

Historically, this subregion was characterizedby broad expanses of shallow bays and brackish tidalmarshes that received substantial amounts of runofffrom many local streams draining narrow valleysbetween ridges of low hills. Major creeks and riversalso ran to the Bay and still do. These include thePetaluma and Napa Rivers in Sonoma and Napacounties, Green Valley Creek in Solano County, andWalnut, Wildcat, and San Pablo creeks in ContraCosta County. The uplands and the relatively flatlands near the Bay often have a high clay content,providing soils suitable for grasslands and oaksavannas.

There have been significant changes to thelandscape of the North Bay, as elsewhere in the BayArea. Most of the tidal marsh that once ringed theNorth Bay has been converted to farmlands or saltponds. The riparian habitat and water quality ofcreeks have been degraded by many decades ofgrazing and woodcutting, but many riparian restora-tion projects are under way to reduce erosion andenhance habitat values within a farming context.Restoration of major floodplains, such as that of theNapa River, is an emerging hallmark of this region,with even larger projects contemplated in thefuture. The Bay margins of Marin present significantopportunities to restore diked baylands to tidal

action. There are several thousand acres of poten-tial salt marsh restoration among the “MarinBaylands.” The former Hamilton Airfield is presentlybeing restored to marshlands. This scale of renew-ing wetlands within a metropolitan context isunprecedented. Other Marin Baylands also presentunique conservation opportunities—particularly ascomponent sites in the expansion of the San PabloBay National Wildlife Refuge. The Fish and WildlifeService is moving forward on plans for this pro-posed expansion.

Suisun Subregion

The Suisun subregion is located in Solano andContra Costa counties and extends from nearChipps Island on the Sacramento River downstreamto the Carquinez Bridge. Suisun Marsh is on thenorth side of the Sacramento River. It is important tonote that below the 10-foot contour the marsh ispart of the Central Valley Habitat Joint Venture’s geo-graphic scope. The Contra Costa shoreline is on thesouth side. Its major watercourses include theSacramento River, and Green Valley, Solano, andWalnut Creeks.

On the Solano side, there are still vernal poolsand moist grasslands on the fringes of Suisun Marsh,particularly to the east and north. A prominent remnant of this seasonal wetland complex is theJepson Prairie Reserve, east of Fairfield in SolanoCounty.

On the Contra Costa side, brackish tidalmarshes along the shoreline extend into the lower

reaches of the major tribu-taries. These marshes areparticularly extensive in theWalnut Creek watershed,which also supports someremnant riparian forest in itstributaries.

Comparing historical topresent conditions in thissubregion, deep bay and shal-low bay habitats havedeclined from about 41,000acres to about 34,000 acres.Much of this change is due tosediment deposits fromSierra Nevada mining in themid-19th century. Some of thedeeper areas have becomeshallow bay, and some of theshallow areas have becometidal flats. Tidal marsh has


A Petaluma River bank is the graveyard of a grain scow that plied the waters in the19th century. JOHN STEERE

also declined significantly in this area. Much of theloss came from tidal marsh being converted to man-aged marsh to provide habitat for wintering water-fowl. These marshes also provide habitat for shore-birds and other wetland-associated wildlife. Themajority of privately-owned managed marshes inthe area are used for duck hunting in the fall andwinter. Private landowners have taken the lead inassuring the protection of the Suisun Marsh.

Adjacent to the baylands, farming and otheractivities have affected most of the moist grasslandhabitat and about one-third of grasslands with ver-nal pools. Farming and stream channelization havegreatly reduced the area of riparian vegetation andwillow groves.

On the Contra Costa shoreline, most of thetidal marshes have been diked, initially for farming.Some have been filled for industrial uses such as oilrefining and power generation. Riparian vegetationhas been stripped from many of the streams. This ismost apparent in the heavily urbanized WalnutCreek/San Ramon watershed, where many miles ofstream channel have been straightened, widened,and lined with concrete.

Central Bay Subregion

The Central Bay subregion includes submergedlands, wetlands, uplands, and the main body of SanFrancisco Bay. It extends along the west shore fromPoint San Pedro to Coyote Point, and along the east

shore from Point San Pablo tothe San Leandro Marina. It fol-lows the northern edge of thecreeks (Crow Creek, AlamoCreek, etc.) that drain theinterior of Contra Costa andAlameda Counties south toAlameda Creek. This regionincludes portions of SanFrancisco, Marin, ContraCosta, Alameda, and SanMateo Counties.

Historically, steep water-sheds draining into broadalluvial fans characterizedthis region. At their baysidemargins, there were smallpockets of tidal marshland,sandy beaches, and naturallagoons, all fed by relativelysmall drainages, with similar-ly scaled areas of tidal flatsand tidal marshes. The near-

Bay habitats in this sub-region reflect the proximityof the ocean more than the other subregions, withstrong marine influence showing in the subtidal andintertidal plant and animal communities. Histori-cally there were few prairies, as there is less flatland between the old marsh line and the hills, butthere were relatively more moist grasslands than inother subregions. The hills, being of mixed geologicorigin and receiving coastal fog, were formerly dom-inated by oak woodlands with occasional stands ofredwood.

Today, this subregion is one of the most urban-ized, with three-quarters of its baylands filled. Tidal


A managed marsh meets a riparian willow grove in the South Bay. JOSH COLLINS

Many Central Bay wetlands have been filled by industrial,commercial, or residential development. PORT OF OAKLAND

marsh acreage has been reduced by over 90 percent,and tidal flat acreage by 70 percent. Large areas ofinterior open space are protected, e.g. the water-shed lands of the San Francisco Water Departmentand East Bay Municipal Utility District, and the park-lands of the East Bay Regional Park District.However, most of the flatland areas of this subregionhave been significantly modified. Restoration hasoccurred on a variety of fronts, but has generallyhad to adapt to the highly urban influences. Unusualrestoration projects have been accomplished,including the “daylighting” (opening) of several cul-verted streams, and restoration of old sewagesludge ponds into marshes.

South Bay Subregion

The South Bay subregion includes the submergedlands, wetlands, and uplands from the southernedges of the Central Bay subregion south to the lim-its of the watersheds feeding the Bay. It abuts theCentral Bay subregion on the west shore at CoyotePoint and on the east shore at the San LeandroMarina. It gets less rainfall than the other subre-gions, and has few major streams; the largestinclude Alameda, Coyote, San Francisquito, SanMateo, and Stevens Creeks. This region includes allof Santa Clara County and portions of Alameda andSan Mateo Counties.

Historically, this subre-gion was characterized bybroad bands of mudflats andtidal marshes on either side ofthe Bay. Between the tidalcreeks were many salt marshponds or pans. Near themouth of San Leandro Creekon the East Bay shoreline wasa complex of large natural saltponds, named Crystal SaltPond on historical maps. Thisfeature was apparently formedby a beach ridge or swash bar,and was a precursor of thesubregion’s man-made saltponds. Along the periphery ofthe baylands were wet grass-lands, and a large area withvernal pools lay near WarmSprings.

Evaporation exceedsprecipitation in the South Bay by a two to one ratio, pro-

ducing less freshwater runoff and much drier condi-tions than in the other subregions. The geology ofthe South Bay also includes more sand and graveldeposits than the other subregions, resulting inbroad alluvial valleys, once dominated by giantsycamores and other riparian vegetation. Theuplands were dominated by shrubs or, at higher ele-vations, woodlands.

This subregion still contains broad valleys withflats adjacent to the Bay, but many have been con-verted to non-habitat uses. Silicon Valley and urban-ization have supplanted the orchards that once cov-ered many of the valleys. Nearly all the moist grass-lands are gone and much of the riparian vegetationhas been removed. Tidal marshes were too saline foragriculture, so they were converted to salt ponds.Sewage treatment facilities, landfills, residential andindustrial uses also reduced the area of natural bay-lands habitats. Restoration projects of many typesare taking place in this subregion, from tidal marshesto riparian woodlands. Watershed planning initiativeshave been particularly active in this subregion.

San Francisco/San Mateo Coast Subregion

The San Francisco/San Mateo Coast subregionincludes the western side of San Francisco and SanMateo Counties, from the submerged and intertidallands of the Pacific Ocean to the crest of the coastal


25,000 acres of Cargill Salt Ponds rim the South Bay; 19,000 acres are now availablefor sale to federal and State agencies. BOB WALKER

range. This subregion has sim-ilarities to the Central Bay, inthat it is characterized byshort, steep watersheds thatlead to pockets of tidal marshwith strong marine influences.However, the Pacific coast isdistinguished by its beauty,prominent rural qualities, andvariety of plant communitiesand wetlands. Tidal and sea-sonal wetlands on the coasttend to be smaller in scalethan those of the Baylands;they are frequently less thanan acre in size. This subregionis a study in dramatic con-trasts, with the heavily devel-oped coastal area of SanFrancisco giving way to therural and relatively wild seg-ments of coastline in SanMateo County. While coastalwetlands are small, the variable topography of thecoastline and the scattering of offshore rocks has ledto a complex mosaic of marine habitats in the inter-tidal zones. Streams lined with willow thickets forminto lagoons; these are generally behind beachesthat fan out along the margins where the creeks enterthe ocean. Inland from the bluffs that characterizethe majority of the San Mateo coast, are coastal ter-races that are primarily in intensive agriculture,while the adjacent slopes of the coastal range areclad in evergreen and mixed hardwood forests.

This portion of the Joint Venture’s regionalscope retains many intact habitats. Over 75 percent

of the land remains wooded—from the redwood andDouglas fir forests found in many of the seawardwatersheds, to the hardwoods along the small, butwell vegetated streams, to the pocket marshes nearthe coast, to the patches of coastal scrub communi-ties near the bluffs and creeks. Restoration work hasbeen occurring in some of the watersheds andstream channels. However, grazing and farmingpractices have been causing excessive sedimenta-tion in the coastal streams, impairing their fisheriescapacity, particularly for salmon, causing siltationeven in several coastal lagoons and marshes thathave been protected in state parks.

Categorizing Wetland Habitats in San Francisco Bay

The habitat categories developed by the SFBJV arebased largely on the extensive and historical ecologi-cal research for the Estuary that was completed bythe San Francisco Bay Area Wetlands EcosystemGoals Project (Goals Project.) Contributors to thisproject, led by researchers at the San FranciscoEstuary Institute (SFEI), with participating scientistsfrom many disciplines, institutions, and agencies,developed a comprehensive set of habitat categoriesfor the Bay and its environs. These were mapped ashabitat types in the Goals Project. They include 14 cat-


An urban wetlands quilt: South Bay salt ponds, looking North toward Bair Island BRADY AERIAL PHOTOGRAPHY

Cowell Ranch Beach along the San Mateo Coast DON COPPOCK

egories of wetlands—tidal flats, tidal marshes andmuted tidal marshes, beaches, lagoons, salt ponds,agricultural baylands, diked/managed wetlands,moist grasslands, grassland/vernal pool complexes,creeks, perennial ponds, and riparian forests and wil-low groves. See Appendix D for descriptions of each ofthese habitat types. The SFBJV has refined these cat-egories into 10 “tracked habitats,” which refers to spe-cific groupings of habitat types whose conditions willbe periodically monitored. Figure 3-1 in the followingchapter shows how the Goals Project classificationstranslate into the tracked habitats of the SFBJV.

The pattern of habitat simplification over timeis indicative of how much wetlands in the Bay Areahave been altered by human activity. The humanmodification of the Baylands (the area once exposedto daily tidal action) that began during the mid-1800s with diking tidal areas to create agriculturallands, salt ponds, managed marshes, and uplandshas drastically changed the mix of habitats in theregion. It has created a curious patchwork of man-made habitats that do provide some biologicalvalue, but lack the diversity found in the complexmosaics of their natural predecessors.


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