Bay Water Trail 
The San Francisco Bay is the largest estuary in western North America, encompassing the San Francisco Bay and the Delta of the Sacramento and San Joaquin rivers. The Estuary’s watershed extends from the ridgeline of the Sierra Nevada mountains to the Golden Gate, including almost 60,000 square miles and nearly 40% of California. It is all one system, however, connected by freshwater outflow to the pacific and by the ebb and flow of ocean tides far upstream into the Delta.
The Estuary’s waters and wetlands are a biological resource of tremendous importance – providing critical winter feeding habitat for over a million migratory birds, a productive nursery for many species of juvenile fish and shellfish, and a year-round home for a vast diversity of plants and animals.
Paddling the Water Trail offers a unique and incredible opportunity to view and learn about the wildlife that lives in and around the Bay. Remember to be considerate of the wildlife you do encounter and avoid disturbing them by maintaining buffer distances. They need their energy for feeding, raising young, and survival.
Watch this video of Sea Kayaking on SF Bay with Environmental Traveling Companions and Naturalist Michael Ellis (footlooseforays.com) to get a glimpse of some of these wild creatures. Film credits to Bearfish Productions.
Birds
The San Francisco Bay has been recognized as a Western Hemisphere Shorebird Reserve Network site of international importance due to the habitat it provides for resident and migratory birds. San Francisco Bay provides the most important complex of wetland habitat for migratory and wintering waterbirds on the Pacific Coast, including wintering habitat for more than 50% of the diving ducks on the Pacific Flyway and more than 500,000 individuals annually.
Early accounts of the San Francisco Bay Area frequently mention the abundance of birds, but the population has decreased due to a combination of many stressors such as habitat loss, pollution, and invasive species. This habitat loss happens in both the summer and wintering areas, resulting in more adverse impacts. Although there are variations, many bird species are sensitive to human disturbance, including disturbance by non-motorized small boats – remember to be considerate of the wildlife you do encounter and avoid disturbing them by maintaining recommended buffer distances.
Pacific Flyway
Many waterfowl use San Francisco Bay in winter months for flocking, feeding, and forming pair bonds in preparation for spring migration to their breeding grounds in Alaska, Canada, and the northern United States. The peak season is November through mid-March, but this can vary year to year. By the time birds stop to rest, their fat reserves are nearly exhausted and San Francisco Bay provides food for them to refuel and continue migration.
Threatened and Endangered Species
Ridgway’s Rail
The Ridgway’s rail (Rallus longirostris obsoletus) is a large, hen-like bird with a long, slightly down-curved bill that is restricted to the marshes around San Francisco Bay. Once abundant, it is currently a federal endangered species and California state fully protected species and is very sensitive to disturbance. Thousands of Ridgway’s rails were eliminated by market hunters from the gold rush until passage of the Migratory Bird Treaty Act. Since then, the loss of over 85% of marsh habitat in the Bay has reduced population numbers.
Populations of Ridgway’s rails are found in remnant salt marshes such as Bair and Greco Islands, along Coyote Creek, and within the Don Edwards San Francisco Bay National Wildlife Refuge. Smaller populations can be found in western Contra Costa, eastern Marin, and northern Alameda Counties; northern San Pablo Bay; along the Petaluma River; and along major creeks and marshes in Sonoma and Napa Counties.
Ridgway’s rails inhabit a range of salt and brackish water marshes. They use the network of small tidal sloughs for foraging and quick escape. The Ridgway’s rail breeding season usually begins in February and can last as long as August. Both male and female share in incubation and chick rearing. Their nests are often found immediately adjacent to a channel, many of which are navigable by shallow-draft non-motorized small boats, making nest sites particularly vulnerable to disturbance. Human disturbance into Ridgway’s rail habitat would likely disturb incubating or brooding birds, potentially reducing reproductive success by breeding pairs (possibly to the point of abandonment of nests, eggs, or young) and possibly destroying active nests. A lost nesting effort, even by a single pair, may have population-level implications for this critically-endangered species.
During very high winter tides, Ridgway’s rails are often concentrated in limited high-tide areas, referred to as “refugia.” Marshes used to have vegetation zones with low, middle, and high marshlands. The high marsh zones act as refuge for many salt marsh animals escaping high tides. These refuge areas have been largely destroyed, resulting in small patches with high concentrations of animals. During high tide events, rail species are particularly vulnerable to predation by mammals and raptors, or other larger birds. If non-motorized small boat users approach high-tide refugia during such extreme tides, they may flush rails into areas where the likelihood of predation would increase. During extremely high winter tides, when much of the marsh plain is inundated, determining the locations of channels, or marsh edge, may be difficult. Boaters should remain at least 50 feet from the edge of the marsh, as demarcated by emergent or inundated vegetation, or other features that may be visible, and not approach vegetation that is not inundated during those times. This means non-motorized small boat users should avoid channels less than 100 feet wide where rails may be present.
Sources/Further Reading
Environmental Protection Agency Endangered Species Fact Sheets
Western snowy plover
The Pacific Coast western snowy plover (Charadrius nivosus nivosus) is a small, threatened shorebird that forages for small invertebrates. Its population has declined due to poor reproductive success, which is likely due to habitat loss and alteration, human disturbance, and predation.
Although snowy plovers often nest on beaches, they also nest on salt ponds and levees in the South Bay. Nesting season is typically March through September. Plover nests are camouflaged and are barely visible to even the well-trained eye. Plovers are polyandrous (the female may breed with more than one male), and the female typically deserts the brood shortly after hatching, leaving the chick-rearing duties to the male.
Human activities and predation are key factors in the decline of breeding sites and populations. Western snowy plovers can be disturbed if boaters disembark near salt ponds or levees – either flushing the adults or stepping on the eggs. If the adult leaves the nest, predation by California gulls, common ravens, northern harriers, or red-tailed hawks may occur. To help protect snowy plovers, please keep a distance of 656 feet (200 meters) from plovers and do not land near salt ponds and levees.
Sources/Further Reading
Environmental Protection Agency Endangered Species Fact Sheet
Protecting Birds
For many wintering waterfowl, the amount of energy reserves built up during the winter months directly impacts migration, survival, and reproductive success. Although there are variations, many waterfowl are sensitive to human disturbance, including disturbance by non-motorized small boats.
Disturbance includes human activity that is an intrusion or interruption in the natural, daily activity of an animal. Usually there is an alert response first, such as the bird stops its normal activity and watches you. This usually escalates to “flushing” in which a bird or group of birds moves away from or flees an approaching threat. In waterbirds this looks like swimming, diving, or flying. Because birds concentrate their activities where there is the best opportunity to maximize energy gain, flushing may reduce the time waterbirds spend feeding or resting and may cause them to be displaced to less than optimal feeding and resting areas, or even abandon foraging habitat. Repeated flushing costs energy, and may have cumulative effects on migratory energy and reproductive success or in a local decline in abundance. Numerous small disturbances may be more damaging than fewer, larger disturbances because birds may not have time to recover between disturbances.
To help waterfowl, maintain a buffer distance of 250 meters, or approximately 800 feet, from congregations of waterbirds to minimize disturbance. If this buffer distance is not possible, users should move steadily through, parallel to, or away from birds.
Sources/Further Reading
USFWS Don Edwards National Wildlife Refuge
Sibley Guide to Bird Life and Behavior by David Allen Sibley
Fish
The Estuary’s waters and wetlands are a biological resource of tremendous importance — providing a productive nursery and hunting ground for many species of fish.
Bat ray
Bat rays (Myliobatus californica) are found in sandy and muddy bays and sloughs, as well as rocky areas. They swim gracefully by flapping their batlike wings, or pectoral fins. The flapping motion, when done in the sand, exposes buried invertebrates that they feed on. They also use their snout to dig for prey and have fused teeth that can crush strong shells, which they then spit out, eating the soft, fleshy parts. Bat rays can be found feeding in the intertidal zone during high tide.
Bat rays mate during the summer months, followed by a gestation period of nine to 12 months. They give birth to two to ten live young. Pups emerge tail first and their stinging spines are covered with a sheath that sloughs off to protect the mother during birth. They can grow to a wingspan of six feet, but this size is uncommon.
Although they have one to three venomous barbed spines at the base of their tail, the docile animals only sting to defend themselves.
For many years, oyster growers trapped bat rays because they thought bat rays ate large numbers of oysters. But recently researchers have discovered that bat rays rarely eat oysters, and that crabs were destroying the oyster beds. The oyster growers were actually causing the destruction of their own oyster beds by trapping bat rays, which eat crabs.
Sources/Further Reading
Baylands Ecosystem Species and Community Profiles: Life histories and environmental requirements of key plants, fish and wildlife. Prepared by the San Francisco Bay Area Wetlands Ecosystem Goals Project.
Northern anchovy
Northern anchovy (Engraulis mordax) is the most abundant fish in San Francisco Bay. This small fish that is only 7 – 9 inches makes up the largest biomass in San Francisco Bay. It is an important food source for larger predators such as California brown pelicans, terns, sharks, seals, Chinook and coho salmon, and other many other fish species. In San Francisco Bay northern anchovies occur from Suisun Bay to South Bay. There is a seasonal influx of the northern anchovy in the spring when water temperatures and plankton production rises in the bay. Adults exit in the fall, although some late-spawned juveniles overwinter within the Bay.
Northern anchovy spawn throughout the year. Females can produce up to 130,000 eggs per year. Depending on the temperature, it takes two to four days for the eggs to hatch. Larvae growth is fast in the warm bay environment. These species are short-lived; most live less than four years. The bay provides good habitat for reproduction because of the ample food for adults and larvae.
Sources/Further Reading
Baylands Ecosystem Species and Community Profiles: Life histories and environmental requirements of key plants, fish and wildlife. Prepared by the San Francisco Bay Area Wetlands Ecosystem Goals Project.
Topsmelt
Topsmelt (Atherinops affinis) are a small fish that many recreational anglers catch and find tasty. There are five subspecies, with only one subspecies (A. affinis affins) found in San Francisco Bay. They can be observed spawning in the Bay and small schools of larvae can often be found near the surface of the water, particularly in tidal basins or sluggish waters. Juveniles are generally found in the open bay or coastal kelp beds. Topsmelt are an important prey item for many birds and fishes and are fished both commercially and by recreational sports fisherman.
Adult topsmelt move into shallow sloughs and mud flats in the spring and summer to spawn, with peaks in May and June. Eggs become entangled in aquatic vegetation and often form clusters. Hatching time varies based on temperature and can range from 35 days to less than 9 days. Topsmelt mature in their second or third year and may live six to nine years.
Sources/Further Reading
Baylands Ecosystem Species and Community Profiles: Life histories and environmental requirements of key plants, fish and wildlife. Prepared by the San Francisco Bay Area Wetlands Ecosystem Goals Project.
Invertebrates
The daily turn of the tides has a profound influence on the San Francisco Bay. Much of the Bay is less than 15 feet deep, so as the tide recedes vast mudflats are exposed. These mudflats support a complex ecosystem of crabs, clams, worms and other invertebrates. When exposed at low tides, these mudflat organisms provide a rich buffet for birds and terrestrial species. Similarly, when the tide turns and these areas become submerged again, aquatic hunters like bat rays and leopard sharks move in to feed.
California horn snail
Although tidal mudflats appear to be bare, they actually support a large community of shellfish, snails, and other invertebrates which are extremely important for wintering waterfowl and shorebirds.
One such invertebrate that lives in the tidal mudflats is the California horn snail (Cerithidea californica), found from Central Baja to Bolinas Bay. It eats decaying plants and algae and benthic diatoms (a one-celled form of algae that lives at lower depths of the water).
Biologists are very interested in the California horn snail because it may be an indicator of the marsh community. The California horn snail is a host for parasitic worms called trematodes. These worms start their life cycle in a snail and eventually end up in birds, without causing harm to the birds. Since trematodes have a complex life cycle, it is a good indicator that predator-prey relationships are working. Biologists studying a marsh in Santa Barbara found that the more birds found at a site, the more trematodes were also found. The California horn snail hosts more than 20 trematode species, making it a species that wetland managers may be able to use for restoration decisions.
Sources/Further Reading
Mammals
Pacific harbor seal
Pacific harbor seals (Phoca vitulina) are the only marine mammal resident in San Francisco Bay year-round. (The California sea lion uses the Bay seasonally for foraging, and some individuals use the floating docks at Pier 39 as a haul-out site). Harbor seals have spotted fur that varies in color. Males and females are about the same size, reaching a maximum of 300 pounds (140 kg). Harbor seals pup March – May and molt June – July. A pup can swim at birth and will sometimes ride on its mother’s back when tired. Adult females usually mate and give birth every year. They may live 25 to 30 years.
Harbor seals tend to congregate on the same terrestrial sites, called “haul-out sites” year after year. Their numbers are highest during the pupping (March – May) and molting (June-July) seasons. Haul-out sites are usually located where there is ease of access to water, proximity to food, and minimal disturbance. Some haul-outs are used year-round, while some are used seasonally. Some sites may be particularly important to seals during pupping and molting as these areas provide shelter from storms. Studies show disturbance by humans has been shown to cause declines in numbers of seals using sites and if sufficiently disruptive, disturbance may cause seals to abandon traditional haul-out sites, and may affect reproductive activities during pupping season.
Disturbance to haul-out sites is often cited as one potential reason for the lack of overall population increase in San Francisco Bay, in contrast with increases seen on the outer coast. Disturbances from kayaks and canoes are comparable to or even greater than those observed for powered vessels. Motorboats tend to maintain constant speed and heading, whereas paddle boats tend to move closer to the shore, approach directly, and change speed and direction frequently. The image of a boat that is slow, quiet, and low to the water may appear more like a predator than other watercraft.
Harbor seals are federally protected under the Marine Mammal Protection Act. The Marine Mammal Protection Act prohibits take, which is harassing, hunting, etc. of a marine mammal. Harassment is any act of pursuit, torment, or annoyance which has potential to injure a marine mammal in the wild, or potential to disturb by causing disruption of behavioral patterns, including migration, breathing, nursing, breeding, feeding or sheltering.
The following guidelines will help you protect Pacific harbor seals from disturbance:
- Maintain minimum distance of 328 feet (100 meters) from haul-out at all times and at least 492 feet (150 meters) from March – July.
- Maintain constant heading and speed while passing haul-out, avoid sudden stop or sudden changes in heading or speed, avoid paddling directly at resting seals.
- If seals show signs of disturbance such as all seals are watching your group or seals begin to approach water, move farther from haul-out.
In the event that you do see an injured marine mammal (information from The Marine Mammal Center):
- Do not touch, pick up, or feed the animal.
- Observe the animal from a distance and keep people and dogs away.
- Note physical characteristics such as size, presence of external ears, and fur color.
- Note the animal’s condition.
- Look for obvious identification tags or markings.
- Determine the animal’s exact location for accurate reporting.
- Call The Marine Mammal Center with as much information as you have.
To Report a Stranded Marine Mammal:
(415) 289-7325 or (415) 289-SEAL
Sources/Further Reading
San Francisco Bay Area Water Trail Final Environmental Impact Report
California sea lion
California sea lions (Zalophus californianus) use San Francisco Bay for foraging, but breed elsewhere (unlike Pacific harbor seals which breed in the Bay). These noisy, intelligent creatures are members of the “walking” seal family whose members have external ear flaps and large flippers that they use to “walk” on land. Males reach 850 pounds and seven feet in length, and females grow to 220 pounds and six feet in length.
In San Francisco Bay, the greatest numbers of California sea lions are found during the winter herring run (December – February). They are opportunistic feeders and will prey mostly on schooling species, but also leopard sharks, shrimp, and crabs. The floating docks at Pier 39 are one of the few known terrestrial locations where sea lions are observed congregating in the Bay.
In the event that you do see an injured marine mammal:
- Do not touch, pick up, or feed the animal
- Observe the animal from a distance and keep people and dogs away
- Note physical characteristics such as size, presence of external ears, and fur color
- Note the animal’s condition
- Look for obvious identification tags or markings
- Determine the animal’s exact location for accurate reporting
- Call The Marine Mammal Center with as much information as you have
To Report a Stranded Marine Mammal
(415) 289-7325 or (415) 289-SEAL
Sources/Further Reading
Marine Mammal Center
Baylands Ecosystem Species and Community Profiles: Life histories and environmental requirements of key plants, fish and wildlife. Prepared by the San Francisco Bay Area Wetlands Ecosystem Goals Project.
Salt marsh harvest mouse
The salt marsh harvest mouse (Reithrodontomys raviventris), is a tiny, endangered mouse that is endemic to San Francisco Bay, meaning it is found nowhere else in the world. Within San Francisco Bay there are two subspecies – a North Bay and a South Bay subspecies. Its scientific name means it is a grooved-tooth mouse with a red belly. The mouse is very small, weighing only 9-14 grams and is approximately three inches in length. Not much is known about the ecology of the mouse as it is secretive and difficult to study.
Unfortunately, the salt marsh harvest mouse has been listed as an endangered species since 1970. The primary threat to the mouse’s survival is habitat loss. Since it is only found around San Francisco Bay, the loss of our marshes has caused a decline in mice numbers. Boaters should not land their craft in marshes to prevent trampling and inadvertently stepping on a mouse or its nest.
Sources/Further Reading
U.S. EPA Endangered Species Facts
