Chapter 3
Chapter 4
Chapter 5
Chapter 6
Chapter 8
Chapter 9
Chapter 10
Main
06/26/98 Draft Report
Process for Establishing Goals
Key Species and Communities
Key Habitats of the Baylands Ecosystem
Baylands Habitats, Past and Present
Technical Considerations for Habitat Restoriation
Monitoring and Research
Implementation Issues
PDF Version
San Francisco Estuary Baylands Ecosystem Goals Draft Report for Public Review June 26, 1998 |
| Figure 5.1 Habitat Classification |  |
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Boundaries between the habitats often are not abrupt. Usually, one habitat intergrades with another in a transition zone called an ecotone. Ecotones can vary in width from a few feet, as at the upper edge of a riprapped shoreline, to hundreds of yards, as at the boundary of high tidal marsh and adjacent grassland. In the baylands, there are ecotones from deep bay to shallow bay, shallow bay to tidal flat, tidal flat to tidal marsh, and so forth. There are also ecotones between the components within a habitat type, and between the saltwater and freshwater extremes of the salinity gradient. The beaches, rocky shoreline, levees, and tidal reaches of adjacent streams are all part of the ecotone from the bayland to the adjacent uplands. Ecotonal areas are important because they support especially diverse groups of plants and animals.
The following section describes the key habitats and notes some of the organisms that use them; it also identifies sites where one can observe good examples of the habitats. Locations of the habitat examples are indicated in Table 5.1 and in Figure 5.2, and information on design and management of many of the habitats is provided in Chapter 8. For more thorough descriptions of the structure, species composition, and associated biota of these habitats, please refer to the appropriate references listed at the end of this report. Consistent with the typology, the descriptions of the key habitats that follow are grouped in three general categories: Bay, Baylands, and Adjacent Habitats.
| Bay Habitats | |
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Bay habitats are intricately tied to the baylands and form part of the baylands ecosystem. They are especially important for aquatic organisms, sea birds, and some mammals, many of which move back and forth between deep and shallow waters. Bay habitats are divided into two categories: areas of deep water and areas of shallow water.
What Is Habitat?
Every plant or animal has a habitat a place where it lives. Habitats vary widely in size from an entire forest to the intestine of a fruit fly. Habitats can be classified in many ways: by dominant plant or animal species, natural environmental factors, or by how the land is managed. Within the baylands, we might discuss a cattail habitat, referring to the dominant plant species that grows there, or seasonal pond habitat, referring to major physical characteristics of the location, or grazed baylands habitat, referring to the unique physical and biological characteristics that result from how the land is managed. Similarly, we might also refer to the communities of plants and animals that occur in the baylands as the cattail community, or the seasonal pond community, or the grazed baylands community.
The plant and animal community associated with one habitat will consist of a different suite of species than that of another habitat, and some habitats clearly support more, and a more diverse array, of species. Some habitats are scarcer than other habitats, and that is one of the reasons some species are scarcer than others.
There are no fixed boundaries for habitats, just as there are no fixed boundaries for environments, communities, or ecosystems. These are all flexible concepts designed to help organize our thinking as we study the natural world.
Deep Bay and Channel
Deep bay and channel is the part of the estuary that is deeper than 18 feet below Mean Lower Low Water (MLLW). It includes the deepest portions of the embayments and the largest tidal channels.
Areas of deep bay and channel are important for Dungeness crab, rock crab, California bay shrimp, and for fishes such as white sturgeon and brown rockfish. They also are migratory corridors through which pass anadromous fishes such as Chinook salmon and steelhead trout.
Deep bay and channel is habitat for several species of water birds including brown pelican, double-crested cormorant, surf scoter, and scaup. Marine mammals such as harbor seal and California sea lion are also found here.
This habitat accounts for about one-third of the Bay surface area and occurs in all four subregions. The deepest area is in Central Bay at the Golden Gate.
Shallow Bay and Channel
Shallow bay and channel includes the area of the Bay where the substrates are entirely between 18 feet below MLLW and MLLW.
Shallow bay and channels are important for many invertebrates, fishes, and water birds. This rich environment is an especially productive feeding area for many fishes including Pacific herring, splittail, northern anchovy, and jacksmelt. It is also an important migratory corridor for anadromous fishes such as steelhead trout and Chinook salmon.
A few of the many bird species that occur in this habitat include western grebe, canvasback, American wigeon, American coot, and Forster's tern. Some of the mammals found here are the harbor seal and California sea lion.
Eelgrass is a particularly important plant species found in the upper reaches of shallow bays and in mudflats. The Bay's only rooted seagrass, eelgrass beds provide feeding, escape, or breeding habitat for many species of invertebrates, fishes, and even some waterfowl. The economically important Pacific herring spawns in eelgrass beds, and least terns forage on small fishes that are found there. Eelgrass also has been found to be an obligate food for black brant along the Pacific flyway.
Shallow bay and channel accounts for about two-thirds of the Bay surface area and occurs in all four subregions. A good example of this habitat is at the northern edge of San Pablo Bay.
| Table 5.1 Locations of Habitat Examples | |
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(see Figure 5.2)
| Site | Habitat Type | Location |
|---|---|---|
| 1. | Deep Bay | Golden Gate |
| 2. | Shallow Bay | San Pablo Bay |
| 3. | Tidal Flat | Grizzly Bay |
| 4. | Mouth of Sonoma Creek | |
| 5. | Marin Shoreline | |
| 6. | South Bay | |
| 7. | Tidal Salt Marsh | China Camp |
| 8. | Heerdt Marsh | |
| 9. | Whittell Marsh | |
| 10. | Greco Island | |
| 11. | Mowry Slough | |
| 12. | Upper Newark Slough | |
| 13. | Tidal Brackish Marsh | Rush Ranch |
| 14. | Brown's Island | |
| 15. | Petaluma Marsh | |
| 16. | Triangle Marsh | |
| 17. | Muted Tidal Marsh | Pacheco Slough |
| 18. | Marta's Marsh | |
| 19. | West End Duck Club | |
| 20. | Charleston Slough | |
| 21. | Lagoon | Tolay Creek |
| 22. | Belvedere Lagoon | |
| 23. | Sonoma Baylands | |
| 24. | Diked Marsh | Cullinan Ranch |
| 25. | Western Marsh and Central Lowlands adjacent to Bahia | |
| 26. | Gallinas Creek | |
| 27. | Fremont Airport | |
| 28. | Area H, Redwood Shores Peninsula | |
| 29. | Managed Marsh | Suisun Marsh |
| 30. | Huichica Unit, Napa-Marsh | |
| 31. | Santa Clara Valley Water District Pond | |
| 32. | Farmed Bayland | Edge of Suisun Marsh |
| 33. | Skaggs Island | |
| 34. | Leonard Ranch | |
| 35. | Twin House Ranch | |
| 36. | Black Point/RenaissanceFaire | |
| 37. | Grazed Bayland | Montezuma Slough Area |
| 38. | Napa River | |
| 39. | Petaluma River | |
| 40. | Ruderal Bayland | Hamilton Antenna Fiel |
| 41. | Edge of Suisun Mars | |
| 42. | Along Highway 237 | |
| 43. | Salt Pond, low salinity | Pond B1/B2, Mtn. View |
| 44. | Pond 1, Mowry Slough | |
| 45. | Pond A9, Alviso | |
| 46. | Salt Pond, mid-Salinity | Ponds A10-A14, Alviso |
| 47. | Ponds 2-8, Coyote Hills | |
| 48. | Ponds 2-6, Mowry Slough-Coyote Creek | |
| 49. | Salt Pond, high salinity | Ponds 10 and 26, Newark |
| 50. | Crystallizers, Newark and Redwood City | |
| 51. | Managed Saline Pond | Inactive Salt Ponds, North Bay |
| 52. | Treatment Pond | American Canyon |
| 53. | Hayward | |
| 54. | Sunnyvale | |
| 55. | Riparian Forest | Suisun Creek |
| 56. | San Antonio Creek | |
| 57. | Sonoma Creek | |
| 58. | Coyote Creek | |
| 59. | Willow Grove | Coyote Hills Regional Park |
| 13. | Native Grassland Community (Remnants) | Rush Ranch |
| 59. | Coyote Hills | |
| 62. | Non-native Annual Grassland | Potrero Hills |
| 63. | Hamilton Field | |
| 64. | Moist Grassland | Near Fairfield |
| 65. | Petaluma River Area | |
| 59. | Coyote Hills, East Side | |
| 67. | Grassland/Vernal Pool Complex | Fairfield Area |
| 68. | Sonoma Creek Area | |
| 69. | Warm Springs | |
| 70. | Coastal Prairie | Brooks Island |
| 71. | Ring Mountain Preserve | |
| 72. | Golden Gate National Recreation Area | |
| 73. | Coast Live-oak Woodland | Carquinez Strait |
| 74. | China Camp | |
| 75. | Angel Island | |
| 76. | Valley Oak Woodland | Green Valley Creek Area |
| 77. | Lower Napa River | |
| 78. | Sonoma Creek Area | |
| 79. | Foothill Oak Woodland | Black Point to Bahia |
| 80. | Mt. Diablo State Park | |
| 81. | Black Diamond Mine Regional Park | |
| 82. | Mixed Evergreen Forest | San Pedro Ridge |
| 79. | Black Point to Bahia |
See map, Figure 5.2 Locations of Habitat Examples
| Baylands Habitats | |
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Baylands habitats encompass all of the lands around the Bay that lie between MLLW and the highest observed tide. They support a broad variety of plants and animals, providing food and shelter, as well as breeding, nesting, roosting, resting, and other opportunities. The discussion below divides baylands habitats into two categories: Tidal Baylands and Diked Baylands.
| Tidal Baylands | |
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The key habitats within the tidal baylands include tidal flat, tidal marsh (both salt and brackish) and lagoon. Each of these key habitats include several habitat components, as described below.
Tidal Flat
Tidal flat habitat includes mudflats, sandflats, and shellflats. It occurs between MLLW and Mean Tide Level (MTL) and supports less than 10 percent cover of vascular vegetation, other than eelgrass. About 90 percent of intertidal flat habitat occurs on the edges of the Bay, and the remainder is associated with tidal channels. A larger proportion of the tidal flats used to occur along the tidal channels in the historical tidal marshes.
During the twice-daily high tides, tidal flats provide foraging habitat for many species of Bay fishes, and during low tides they are the major feeding area for shorebirds. Mudflats, in particular, are rich in food items.
Mudflats comprise the largest area of tidal flat habitat. These areas of fine-grained silts and clays support an extensive community of diatoms, worms, and shellfish, and more complex vegetation including green algae, red algae, and sea lettuce. Eelgrass, described previously under shallow bay and channel habitat, also can be a component of mudflats.
Tidal flat occurs in each of the Bay's four subregions. However, there tends to be a natural decrease in the amount of tidal flat in brackish or freshwater areas compared to the more saline parts of the Bay. This is because marsh vegetation grows lower in the intertidal zone under fresher conditions, such that the part of the zone that would be tidal flat is occupied by tidal marsh. As a result, about one-third of the Bay's tidal flat habitat is in the North Bay, and more than one-half is in the South Bay. Accordingly, the South Bay is considered to be the region's most important area for shorebirds, which mainly feed across the tidal flats. Examples of tidal flat exist in Grizzly Bay, along the Marin Shoreline, at the Emeryville Crescent, and throughout much of the South Bay.
What Is a Tidal Datum?
The word "tides" most commonly refers to the alternating rise and fall of the oceans. The National Ocean Survey (NOS) measures every tide at two tide stations in the San Francisco estuary. These measurements are used to estimate average heights of the tides for each tidal epoch, which is the 19 year interval between alignments of the moon, the sun, and the earth. If the moon is full today, then it will be full again on this date in 19 years. The estuary experiences two high tides and two low tides most days. All four of the tides in a day are different heights. This is called a "mixed tide."
The average local heights of the tides are called tidal datums. The average height of the higher of the two high tides is called local Mean Higher High Water (MHHW). The average of all the high tides is called local Mean High Water (MHW). There are many other datums, including Mean Lower Low Water (MLLW), Mean Low Water (MLW), and Mean Tide Level (MTL), which is midway between MHW and MLW. Mean Sea Level (MSL) is the average of all the tide measurements for a tidal epoch. Local MLLW is the zero datum of the tides, or zero tidal elevation. "Minus tides" are below MLLW.
Many things affect local tide height. Besides the moon, there is wind, barometric pressure, the shape of the Estuary, and distance from the Golden Gate. Tide height varies within tidal marshes because of friction in tidal channels.
Tidal datums have also been used to measure land elevations. Values for Mean Sea Level in 1929 were adopted as the National Geodetic Vertical Datum (NGVD 29), or zero elevation for measuring land height. Benchmarks were established throughout the United States marking local elevations relative to NGVD 29. Since then, disturbance and loss of many benchmarks has warranted a new datum. The NGVD 29 is being replaced by the North American Vertical Datum of 1988 (NAVD 88), and new geodetic datums are being planned to make use of improved surveying technology.
Tidal datums must be recalculated periodically because sea level is changing. During the last few thousand years, sea level in the Estuary has been rising at an average rate slightly greater than 0.1 inch per year, or about 1 foot per century. Tidal datums are recalculated for each new tidal epoch, beginning in 1929.
Tidal Marsh
This habitat occurs throughout the Bay in undiked areas that are open to complete tidal action. It occurs from the top of the intertidal zone, at the maximum height of the tides, to the lowest extent of vascular vegetation, which is lower in the fresher reaches of the ecosystem, such as in Suisun, and in the tidal reaches of local rivers and streams.
In the more saline parts of the North, Central, and South bays, tidal marsh is referred to as tidal salt marsh. In the more brackish areas where there is significant freshwater influence as in Suisun, along the Petaluma and Napa rivers, and at the mouths of several streams in the South Bay it is referred to as tidal brackish marsh.
Both types of tidal marsh are typically characterized by three general zones of vegetation, each of which is related to tidal elevation. Low tidal marsh occurs between the lowest margin of the marsh and Mean High Water (MHW). Middle tidal marsh occurs between MHW and Mean Higher High Water (MHHW). High tidal marsh occurs between MHHW and the highest margin of the marsh.
Tidal marshes have a variety of important habitat components including creeks and tidal channels, ponds, and transitional pannes. Large tidal channels and their smaller tributaries form drainage networks that distribute tidal waters and upland runoff throughout the marsh. Where the marsh plain is fairly level, they tend to be sinuous, but where it slopes more steeply, the channels tend to be straighter. Channel density (e.g., the amount of channel habitat per acre of marsh plain) is directly related to tidal prism, the volume of water that flows into and out of the marsh. A high marsh with a small tidal prism typically will have fewer channels than does a low marsh with a larger tidal prism. Also, channel density seems to be related to salinity; salt marshes generally have denser networks of tidal channels than do brackish marshes.
Marsh ponds and transitional pannes are also unique features of tidal marsh. The term marsh pond refers to natural ponds between about six and nine inches deep that form in the high marsh plain between tidal channels. These ponds are sometimes referred to as drainage divide ponds. They only fill with tidal water during very high tides. They may be hypersaline in late summer, but they do not develop thick deposits of salts as do natural or commercial salt ponds. Brackish marshes, such as at Petaluma Marsh, have fewer but larger drainage divide ponds. In salt marshes, such as at China Camp and at Mowry Slough (particularly in the historical portions), ponds tend to be smaller but more abundant.
Transitional pannes are natural basins less than about six inches deep that occur along the ecotone between tidal marsh and the adjacent upland. They tend to be elongate, with the long axes parallel the marsh/upland boundary. Local influences of topography, microclimate, groundwater, and freshwater runoff affect the salinity of these pannes; however, in general, pannes tend to be hypersaline in tidal salt marshes and saline in tidal brackish marshes. Transitional pannes occur in the area adjacent to the Mare Island dredge ponds, at the edge of the Emeryville Crescent, and at the east end of the tidal salt marsh that fringes Highway 37.
When a tidal marsh receives less than full tidal flow because of a physical impediment such as a channel constriction or culvert or other water control structure, it is referred to as a muted or damped tidal marsh. These marshes exhibit many of the same features as fully tidal marshes, but they often lack their full range of vegetation diversity. Accordingly, they typically are less valuable as fish and wildlife habitat.
Tidal Salt Marsh- California cordgrass and common pickleweed are the dominant plant species in tidal salt marsh. California cordgrass is usually the primary colonizer on broad tidal mudflats that fringe tidal marsh plains, and it occurs in virtually pure stands in the low marsh between about MTL and MHW. Midway within this tidal range, it intermixes with annual pickleweed, especially in depressions in the marsh plain.
In the middle tidal salt marsh, at elevations near and above MHW, California cordgrass yields to common pickleweed. This perennial succulent dominates the salt marsh plains around the Bay. In the high tidal salt marsh, between about MHW and the maximum extent of the tides, common pickleweed is found in association with peripheral halophytes including salt grass, salt bush, and alkali heath.
Additional plant species on tidal marsh plains include salt grass, fat hen, marsh rosemary, alkali heath, and jaumea. Natural and man-made levees support coyote brush and gumplant. Dodder, a parasite on common pickleweed, exists in small patches in some marshes, generally where tidal circulation is reduced, and in large sheets in some marshes in the South Bay.
Tidal Brackish Marsh occurs in parts of the Bay where freshwater runoff reduces salinities. Salinities vary markedly from season to season and from year to year, depending largely on rainfall patterns, and the plant communities of brackish marsh reflect these changes.
Low marsh is dominated by cattails and California bulrush. Middle marsh is dominated by a very diverse assemblage of plant species including bulrushes, spike rush, Baltic rush, silverweed, and salt grass. High marsh, at or above MHHW, is characterized by a varied group of salt-tolerant plants including common pickleweed, saltgrass, gumplant, and alkali-heath.
The high marsh vegetation in a tidal salt marsh or tidal brackish marsh typically intergrades with upland plant species in an area referred to as the marsh/upland ecotone. The width of this zone is determined primarily by the slope of the land; in flatter areas such as in Suisun, it may be hundred of yards wide, whereas in the Central Bay, with its relatively steep shorelines, the zone is usually narrower. The marsh/upland ecotone is very important ecologically, as it is characterized by a diverse assemblage of vegetation and may provide especially valuable habitat for many species of wildlife.
The development of the baylands has severely affected tidal marshes, especially in the high marsh zone and in the high marsh/upland ecotone. Filling marshes and isolating the remnants from sediment and freshwater flows from adjoining watersheds has greatly reduced tidal marsh plant diversity; past floral accounts of the Bay note a much greater diversity of marsh plants than exists today. Research done by the Project's Plant Focus Team indicates that more than fifty plant species found in the Bay marshes at the turn of this century are now extinct or exist only in isolated populations. Most of these species resided in the high marsh or in the marsh/upland ecotone. Locally extinct species include Point Reyes bird's beak, salt marsh owl's clover, and smooth goldfields (all extirpated in the South Bay); and California sea-blite and California saltbush (extirpated throughout the estuary).
Today, rare plant species of tidal marsh include Point Reyes bird's beak (in Richardson and San Pablo bays, and Suisun Marsh), soft bird's-beak, Suisun thistle, Mason's lileaopsis, and Delta pea.
Tidal marshes provide a complex habitat for an array of fish and wildlife. Common fishes of South and Central Bay marshes include topsmelt, arrow goby, yellowfin goby, and staghorn sculpin. In the North Bay, gobies, sculpins, and three-spined stickleback are common. In Suisun Bay, splittail, Delta smelt, and longfin smelt occur in the marsh channels.
Some bird species associated with marshes include the California clapper rail, California black rail, salt marsh yellowthroat, willet, Suisun song sparrow, San Pablo song sparrow, Alameda song sparrow, northern harrier, red-tailed hawk, and short-eared owl. Small mammal species that are dependent on tidal marsh include the Suisun shrew, salt marsh harvest mouse, and salt marsh wandering shrew. Harbor seals utilize tidal marsh, especially areas adjacent to sloughs in the South Bay, as resting or haul-out sites during high tides. With about 80 percent of the region's original amount of tidal marsh filled or converted to non-tidal habitats, and with many of the remaining marshes severely degraded, many marsh-associated species of fish and wildlife are listed as threatened or endangered, or are known or believed to be experiencing population declines.
Tidal marsh occurs throughout the Project area, but the largest areas are on the northern edge of San Pablo Bay and along the Petaluma River. Suisun Bay, too, supports a substantial acreage of tidal marsh, while Central Bay supports relatively little. Examples of tidal salt marsh are found at China Camp, Heerdt marsh, Whittell Marsh, Greco Island, Mowry Slough, and Upper Newark Slough. Examples of tidal brackish marsh are at Brown's Island, Rush Ranch in Suisun Marsh, Petaluma Marsh, and in the South Bay at Triangle Marsh. Examples of muted tidal marsh include the marshes near the mouth of Pacheco Slough in Suisun, Marta's Marsh and the West End Duck Club in the North Bay, and Charleston Slough in the South Bay.
Lagoon
A lagoon is an impoundment of surface water that is subject to at least occasional or sporadic connection to full or muted tidal action. The impoundment may or may not receive a creek or other form of uplands runoff, and it can be natural or artificial.
Lagoons support many of the same species of aquatic invertebrates and fishes that occur in nearby shallow Bay and channel habitats. They also provide feeding or loafing habitat for a variety of water birds such as brown pelican, canvasback, ruddy duck, bufflehead, and scaup. Lagoons may be sites of early colonization by introduced aquatic species.
Lagoons occur in North Bay, in Central Bay, and in South Bay, but they are nearly absent in the Suisun area. Examples are the lagoons at Tolay Creek and Tiburon, and Sonoma Baylands.
| Diked Baylands | |
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Diked baylands exist in the parts of the Bay that once were tidal but are now isolated from the tides. Their physical origins are generally similar in that most were initially diked or "reclaimed," beginning in the mid 1800s, for some kind of agricultural use or for salt production. Reclamation typically involved the construction of earthen dikes along the margins of the marsh plains where they bordered mudflats or major tidal creeks.
Diking for agriculture resulted in a variety of major landscape changes. Initially, the most obvious change was the reduction or elimination of tidal marsh vegetation as the land was farmed. After diking, aerobic decomposition and dewatering of the peaty marsh soils caused the diked land surface to settle or subside. Subsidence was greatest in areas that correspond to the middle areas of the historical marsh plains, where the peat soils are deepest. In some cases, as in the Suisun Marsh, the historical topography eventually became inverted areas that once were high marsh drainage divides with ponds became low, isolated depressions, lower than the relict channels and natural levees. Tidal channel topography typically persisted as sinuous swales.
By the early 1900s, many diked farmland operations began to fail because the costs of compensating for increased subsidence and dike maintenance at times exceeded the return on agricultural benefits. Many of the farmed lands that went out of production decades ago have become diked marsh, managed marsh, or some other type of habitat including salt pond.
Key habitats within the diked baylands include diked marsh, managed marsh, farmed bayland, grazed bayland, ruderal bayland, salt pond, managed saline pond, managed seasonal pond, and treatment pond.
Diked Marsh
Diked marsh consists of areas within historical tidal marshes that have been isolated from tidal influence by dikes or levees and converted to non-tidal salt marsh or non-tidal brackish marsh. These diked areas are not actively managed for plants or wildlife, salt production, or agricultural products, although they might have been subject to such management in the past.
The plant communities of diked marsh vary greatly from site to site and can resemble those of local tidal salt marsh, tidal brackish marsh, or non-tidal perennial freshwater marsh. Diked marsh, however, usually has fewer native species than its analogous natural tidal plant communities, and often a larger component of exotic plant species. Native plant species common to diked marsh areas include common pickleweed, alkali bulrush, bulrush, and cattail.
Diked marsh provides habitat for a variety of waterfowl and shorebirds and for small mammals. Although some areas provide reasonably high wildlife value, especially where persistent ponds form during the winter months (as at some dredged material disposal sites), overall, most diked marshes would provide better habitat for more species if they were managed as tidal systems.
Examples of diked marsh occur at the Western Marsh and Central Lowlands adjacent to Bahia, Gallinas Creek, the abandoned Fremont Airport, and Area H on the Redwood Shores Peninsula.
Managed Marsh
Managed marsh consists of diked areas where the distribution of surface water is controlled to support a desired community of plants and wildlife. Managed marshes are located in private duck clubs and on publicly owned wildlife management areas and refuges.
Suisun Marsh is the largest managed marsh in the estuary. Its 52,000 acres of diked wetlands are managed primarily to provide wintering feeding habitat for migratory waterfowl and, in dry years, it has supported more than one-quarter of the Central California waterfowl population. It has a diversity of habitats due to varying water and land management practices. Marsh management is usually designed to favor mixtures of shallow submerged mud, and plants such as bulrushes, tules, cattail, brass buttons, fat hen, and barley. Other species have colonized these brackish wetlands, including goosefoot, dock, purslane, and pepper grass.
Managed marshes, although much smaller than Suisun Marsh, also exist in the North Bay and South Bay. The vegetation in the North Bay marshes includes many of the same species that are in Suisun Marsh, but salt tolerant species predominate. Likewise, the plant species of the South Bay managed marshes are mostly those of the tidal salt marsh community.
Managed marshes are typically managed to provide habitat for waterfowl, especially mallard, pintail, and northern shoveler. They also provide habitat for many species of shorebirds and other birds. For example, more than 20 species of shorebirds occur in Suisun Marsh, along with many species of hawks and owls. Mammal species that occur in Suisun Marsh include river otter, tule elk, and salt marsh harvest mouse, one of about a dozen species of rodents that occur there.
Examples of managed marsh are Suisun Marsh, the Huichica Unit of the Napa-Sonoma Marsh, and the Santa Clara Valley Water District pond adjacent to Coyote Creek.
Farmed Bayland
Farmed bayland is land that consists of diked, former tidal salt marshes or tidal brackish marshes that are intensively cultivated for agricultural production, primarily oat hay. Most farmed baylands support seasonal ponds and some wetland and upland plants. If these lands were not in active cultivation, they would support a diverse array of wetlands and uplands plants.
During the wet season, large areas of farmed bayland become waterlogged or inundated. The patterns of waterlogging and inundation depend principally on the relict tidal marsh topography, the extent and effectiveness of artificial drainage, soil permeability, and the amount and seasonal distribution of rainfall. Successfully raising a crop such as oat hay requires careful management of ground water levels, soil salinity, and levees.
Until the middle part of this century, water levels on farmed baylands were regulated by gravity-driven systems of drainage ditches through which flowed ground and surface water from fields to the adjacent marshes via one-way flapgates. These systems had limited efficiency, and low places in the fields (swales of relict tidal creeks and relict marsh ponds) often remained poorly drained well into the crop growing season. Today, subsidence of diked agricultural baylands has increased to the point at which gravity-driven drainage systems are ineffective, and farmers actively pump water from the fields.
After many years of this kind of land management, baylands soils tend to become subsaline to nonsaline and support a range of marsh plant associations in addition to cultivated crops. Agricultural fields that are disked annually typically support a mixture of native annual wetland plants (e.g., popcornflower, rushes, Eryngium), and non-native annuals (e.g., loosestrife, brass buttons, barley) and perennials (e.g., birdsfoot trefoil and Agrostis).
Farmed baylands provide habitat for many species of wildlife. They are important as roosting and feeding habitat for wintering shorebirds including long-billed dowitcher, marbled godwit, western sandpiper, and for waterfowl such as mallard and northern pintail. Other bird species commonly found on farm fields include snowy egret, black-crowned night heron, northern harrier, horned lark, savannah sparrow, red-winged blackbird, and western meadowlark. Some of the mammal species utilizing this habitat include striped skunk, California vole, California ground squirrel, black-tailed deer, and coyote.
Within farmed baylands, areas of shallow seasonal ponds are the most important habitats for shorebirds and waterfowl. These ponds typically are less than six inches deep, have feathered edges, and a minimum of emergent vegetation. Shorebirds, in particular, use these ponds during high tides when they are unable to forage on nearby tidal mudflats. The areal extent and duration of ponding vary markedly from year to year and are highly influenced by pumping and rainfall patterns. Ponds with the highest habitat values are those that occur every year and which are frequently or continuously inundated during the wet season.
Nearly all of the farmed baylands are in the San Pablo Bay subregion, although some farming also continues in the South Bay and in Suisun Marsh. Examples of this habitat exist at the northwestern edge of Suisun Marsh and at Skaggs Island, Leonard Ranch, Twin House Ranch, and Black Point/Renaissance Faire.
Grazed Bayland
Grazed bayland consists of diked areas that are actively managed as pasture for livestock including cattle, sheep, and horses. Pastures in grazed baylands that are not frequently cultivat
ed or mowed provide abundant cover and food, allowing year-round use by more species of wildlife compared to intensively farmed areas.Like farmed baylands, grazed baylands also may support wetland plants and shallow seasonal ponds in the wet season that are important to shorebirds and waterfowl. Most of this habitat is in the North Bay near the Petaluma River, and the Napa River. In Suisun Marsh, large expanses occur adjacent to Montezuma Slough.
Ruderal Bayland
Ruderal bayland is similar to diked marsh except that in all cases upland grasses and other vegetation such as wild mustard, fennel, and poison hemlock are a dominant component of the plant community. Some ruderal baylands, especially the wetter, lower portions of some sites, support a variety of amphibians, reptiles, birds, and small mammals.
This habitat type is not widespread in the baylands. Examples occur at the antenna field next to Hamilton Field, at several areas on the periphery of Suisun Marsh, and along Highway 237 near Gold Street.
Salt Pond
Salt ponds are large-scale, persistent hypersaline ponds that are intermittently flooded with Bay water. They occur within the historical areas of tidal salt marsh in the North Bay and South Bay.
Historically, there were natural salt ponds along the edge of the Bay, primarily restricted to a relatively narrow reach near San Lorenzo Creek and Mt. Eden Slough near Hayward. Native Americans obtained salt from these ponds for their own use and for trade; later, so did the region's Spanish and other settlers. In the mid-1800s, as the demand for salt rose, the first artificial salt ponds were developed in this area as extensions and improvements of the natural salt ponds. Today, artificial salt ponds have entirely displaced their natural forerunners, and no natural, true salt-crystallizing ponds remain in the Bay.
The process of making salt in the artificial ponds involves moving Bay water through a series of ponds, known as concentrators or evaporators, over a period of six or seven years, during which time solar evaporation of the water increases its salinity from about 35 parts per thousand (ppt) to more than 180 ppt. The precipitation of sodium chloride salt from the highly saline water, or brine, takes place in diked ponds known as crystallizers.
For the purposes of describing and comparing the habitat functions of various salt ponds, the Project's bird focus teams developed arbitrary salinity classifications, based on salinity. Low salinity ponds usually have a salinity range of less than 60 ppt. Medium salinity ponds usually have a salinity range between 60 and 180 ppt. High salinity ponds usually have a salinity range greater than 180 ppt, but are less saline than crystallizers where salinities approach 360 ppt at saturation.
Salt ponds support a distinctive and highly specialized salt-tolerant to salt-loving biota consisting of microalgae, photosynthetic bacteria, and invertebrates (e.g., brine fly and brine shrimp), but no vascular plants. The dominant species are single-celled green alga and numerous species of blue-green and other bacteria. Ponds with salinities closer to marine salinities support macroalgae such as sea lettuce and marine plankton.
Salt ponds, especially those with low to mid salinities, provide important habitat for many species of resident and migratory wildlife, particularly birds. They are of primary importance to migratory shorebirds and waterfowl, and they also provide year-round foraging habitat for a number of resident species such as American avocet, black-necked stilt, and killdeer. These and several other species, including California gull, western gull, Caspian tern, Forster's tern, killdeer, and western snowy plover, nest on salt pond levees and islands. In all more than forty species of birds are considered to be common on salt ponds. Crystallizers provide habitat for wildlife including shorebirds, gulls, and other waterbirds; however, given their comparatively high salinities, their habitat quality for most species of birds is not as high as lower-salinity ponds.
The construction of artificial salt pond habitat in the Bay enabled increased populations of many bird species. These species include eared grebe, white pelican, snowy plover, Caspian tern, Forster's tern, Wilson's phalarope, California gull, American avocet, and black-necked stilt. The populations of some of these species would be greatly reduced or even extirpated from the Bay if salt ponds or shallow saline ponds were to disappear.
All of the salt ponds that are actively producing salt for commercial purposes are in the South Bay, south of the San Mateo Bridge. In this subregion, there are two crystallizer complexes, one in Redwood City and one in Newark. In the North Bay, the complex of salt ponds west of the Napa River no longer produces salt, with last harvested from the crystallizer complex on the east side of the Napa River in about 1990.
Managed Saline Pond
The managed saline pond habitat designation refers to non-tidal, saline ponds actively managed for shorebirds and waterfowl. This term currently applies only to the inactive salt ponds in the North Bay, although the management of those ponds is not yet able to maximize habitat values. It also would apply to the salt ponds in the South Bay if they were managed for shorebirds and waterfowl rather than for salt production.
Under the ideal regime of intensive management, saline ponds would be managed in complexes, with water depth and salinity varying from pond to pond. During some parts of the year, some ponds would be drawn down to increase habitat diversity; some would likely be managed to provide nesting habitat for plovers, terns, and other birds by exposing the pond bottoms. Pond salinities generally would be in the low and mid salinity ranges.
Managed saline ponds provide shallow water habitat for a diverse group of fishes and water birds, including most of the species that occur in salt ponds. A primary difference between salt ponds and managed saline ponds is that the latter are managed to maximize wildlife habitat, not to produce salt. As a result, managed saline ponds are expected to increase the carrying capacity for many species, compared to an equal area of salt pond.
Managed Seasonal Pond
This habitat type would occur in the future in baylands that are now mostly classified as farmed, grazed, or ruderal. This habitat designation refers to diked areas that would be covered by large expanses of shallow seasonal ponds of varying depths. The ponds would comprise perhaps 25 to 50 percent of the land area and would be interspersed among slightly higher features that could support a mix of fairly sparse, low-growing seasonal wetland and upland vegetation.
Managed seasonal ponds would be managed as habitat for wildlife, primarily shorebirds and waterfowl. Management could vary considerably, and would include both passive management designed to provide wildlife functions with no or little ongoing maintenance and active management.
The community of wildlife species that would occur in managed seasonal pond habitat would be similar to that of farmed, grazed, or ruderal baylands. Significantly, however, habitat management would greatly increase the carrying capacity of the land for key species of shorebirds and waterfowl.
Treatment Pond
The treatment pond designation refers to diked, perennial habitat that has been constructed to treat industrial discharges, sewage, or runoff. It supports relatively little vascular vegetation. Most of the treatment ponds are parts of municipal wastewater treatment works. They store treated effluent before it is discharged to the Bay. Treatment ponds provide habitat for several groups of waterbirds, especially waterfowl such as scaup, bufflehead, and American coot. Examples are the wastewater treatment facility ponds at American Canyon, Hayward, and Sunnyvale.
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There are several major plant communities that occur in the bay area mostly outside of the baylands. Those that exist closest to the baylands are described briefly here because they are part of the baylands ecosystem and are important habitats for many of the baylands' far-ranging wildlife species. The project's species narrative report, scheduled for release in the fall of 1998, will provide considerably more detail on these habitats.
Riparian Forest
The term riparian refers to the banks of water courses, and riparian forest occurs on the terraces, flood plains, and levees of the estuary's tributary streams. The dominant species vary among the subregions but may include cottonwood, California bay laurel, coast live oak, valley oak, willow species, white alder, maple, and western sycamore. Near the estuary, red willow and arroyo willow dominate riparian vegetation. Common understory species are elderberry, wild rose, and blackberry.
Riparian forest is considered to be the most valuable of habitats available to wildlife. Water, food, and cover are all supplied in this habitat type. The complexity of microhabitats created by the layering of trees, shrubs, and herbaceous and aquatic vegetation promotes high wildlife species diversity.
Riparian forest enhances the functions of adjacent fish and wildlife habitats such as grasslands or agricultural fields. It is most valuable when it exists in an unbroken corridor along a stream channel, leading through a watershed and across the valley floor and flatlands to the baylands.
A few representative wildlife species that use this habitat include California newt, ring-necked snake, wood duck, great-horned owl, tree swallow, northern oriole, ornate shrew, broad-footed mole, and deer mouse. Examples of riparian forest exist along Suisun Creek, San Antonio Creek, Sonoma Creek, and Coyote Creek.
Willow Grove
This is a stand-alone patch of willow trees in an area that is not directly associated with a riparian zone. It may be associated with ground water discharge, perennial ponds, or seasonal ponds. In some instances, particularly in the south bay, willow groves also occur where intermittent streams terminate before reaching the bay. The dominant species is arroyo willow, and associated species include california blackberry and silverweed.
Willow groves support many species of amphibians, birds, and small mammals that also frequent the baylands. Representative species include pacific treefrog, snowy egret, black-crowned night heron, northern harrier, raccoon, and striped skunk. One of the few remaining examples of willow grove exists at the coyote hills regional park.
Grassland
Vegetation dominated by grasses and sedges was widespread along the shores of the estuary prior to European settlement. Native perennial grassland predominated near the estuary on valley floors and hillslopes. These grasslands were composed primarily of perennial bunch grasses and rhizomatous grasses, dominated by purple needlegrass and creeping wild rye. Examples of remnants of this community are at Rush Ranch and Coyote Hills. Today, several types of grassland occur in the Bay Area.
Grasslands near the edge of the estuary are frequented by many species of wildlife that also occur in the baylands. In summer, amphibians such as the tiger salamander aestivate in grassland soil to avoid heat stress. In winter, grasslands provide important foraging habitat for cranes, geese, and large and small migratory shorebirds. Other species that are commonly found include American kestrel, turkey vulture, burrowing owl, western meadowlark, and valley pocket gopher.
Non-native annual grassland - The introduction of European grazing and agriculture in the 1800s shifted the region's grassland communities from native perennials to Eurasian non-native annuals; dominant species of these communities are wild oats, soft chess, ripgut brome, and Italian ryegrass. Non-native annual grassland occurs on the interior valleys surrounding the baylands, on the unforested hillslopes with southwest aspect, and on the alluvial plains. Examples of non-native grassland exist at Potrero Hills, Hamilton Field, and Coyote Hills.
Moist grasslands exist in wet soils that tend to be saturated for relatively long periods. In the Bay Area, these soils exist primarily adjacent to the baylands in the areas of nearly flat topography. Dominant species may include Italian ryegrass, Baltic rush, iris-leaved rush, Santa Barbara sedge, and creeping wildrye.
Moist grasslands attract more species of wildlife than do drier areas. Representative species include western toad, western skink, western harvest mouse, meadowlark, horned lark, and savannah sparrow. Grasslands with vernal pools support many of the same species as do moist grasslands.
Historically, moist grasslands existed in large expanses near Suisun Marsh, in the upper reaches of Sonoma Creek and the Petaluma River, and adjacent to much of the baylands in the South Bay. Today, examples of this habitat exist near Fairfield, in the Petaluma River area, and at the eastern base of Coyote Hills.
Grassland/Vernal Pool Complex is an area of non-native annual grassland where there are vernal pools. Vernal pools are surface depressions usually less than 6 inches deep that are underlain by an impervious substrate of natural materials. They tend to be wetted by direct rainfall or nearby runoff during the wet season, and desiccated by evapotranspiration early in the dry season. Typical native vernal pool species include goldfields, popcorn flower, Navarretia, and Downingia.
Some wildlife species associated with vernal pools include fairy shrimp, tadpole shrimp, California tiger salamander, western spadefoot, common garter snake, American avocet, and black-necked stilt. Some waterfowl, especially mallard and cinnamon teal, nest in this habitat where there are pools. Small mammals, including California vole and black-tailed hare, also occur here.
Historically, grasslands with vernal pools occurred on large areas adjacent to Suisun Marsh, west of Sonoma Creek, and in the Warm Springs area in South Bay. Although much of the grassland/vernal pool complex near Fairfield has been disturbed by farming or is filled, examples of this habitat still exist there and at Sonoma Creek and Warm Springs.
Coastal prairie is a type of grassland that occurs in limited distribution near the Bay in areas that are frequently exposed to moist marine air and which have clay soil. Dominant species include Douglas iris, reedgrass, oatgrass, and hairgrass. Examples occur at Brooks Island, Ring Mountain Preserve, and at the Golden Gate National Recreation Area.
Oak Woodland
Vegetation with an overstory dominated by oak trees is common throughout California's valleys, foothills, and lower mountain ranges. In the Bay Area, there are three recognized types of oak woodland, based on species dominance.
Oak woodlands provide important habitat for many species of amphibians, reptiles, birds, and small mammals that frequent the baylands. Some representative species include ensatina, southern alligator lizard, gopher snake, red-tailed hawk, california quail, acorn woodpecker, scrub jay, california ground squirrel, audubon's cottontail, and black-tailed deer.
Coast live oak woodland occurs on hillslopes with thin soils and moderate to large amounts of rainfall. The dominant species is coast live oak. Associated species include madrone, California blackberry, creeping snowberry, cream bush, and poison oak. Examples exist on the north-facing slopes along the Carquinez Strait, at China Camp, and on Angel Island.
Valley oak woodland occurs on areas of the alluvial plains, valleys, and piedmonts adjacent to the baylands. The dominant species is valley oak. Associated species include creeping wild rye and Santa Barbara sedge. This community is not widespread in the Bay Area; examples exist along Green Valley Creek near Cordelia, along the lower Napa River, and along Sonoma Creek near Schellville.
Foothill oak woodland occurs on hillslopes with deep soils and small to moderate amounts of rainfall. The dominant species is blue oak. Associated species include digger pine, manzanita, deerbrush, coffeeberry, and pink-flowered currant. This community is not widespread on the lands near the Bay. Examples exist on the ridge at Black Point and Bahia, at Mt. Diablo State Park, and at Black Diamond Mine Regional Park near Antioch.
Mixed Evergreen Forest
Mixed evergreen forest is mostly restricted to north-facing hillslopes in the North Bay and Central Bay areas. The dominant species include California bay laurel, bigleaf maple, and madrone. Associated species are coyote brush, California huckleberry, poison oak, and deer brush.
This vegetation complex provides habitat for a variety of wildlife. Some representative species are common garter snake, western fence lizard, Nuttall's woodpecker, wrentit, dark-eyed junco, Cooper's hawk, hermit thrush, purple finch, dusky-footed woodrat, brush rabbit, and gray fox. Examples of mixed evergreen forest occur in the headward reaches of north-facing draws of San Pedro Ridge near China Camp and on the ridge at Black Point and Bahia.
