
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
Marine Mammal Center
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
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.
Photo of Salt Marsh Harvest Mouse by Judy Irving © Pelican Media
Sources/Further Reading
U.S. EPA Endangered Species Facts