The Farallon Islands are an important reserve protecting a huge seabird colony. The islands' position in the highly productive California Current and eastern Pacific upwelling region, as well as the absence of other large islands that would provide suitable nesting grounds, result in a seabird population of over 250,000. Twelve species of seabird and shorebird nest on the islands; western gull, Brandt's cormorant, pelagic cormorant, double-crested cormorant, pigeon guillemot, common murre, Cassin's auklet, tufted puffin, black oystercatcher, rhinoceros auklet, ashy storm-petrel, and Leach's storm-petrel. Since the islands were protected, common murres, which once numbered nearly 500,000 pairs but suffered from the egg collecting, oil spills and other disturbances that had greatly reduced their numbers, recovered and climbed from 6,000 birds to 160,000. Additionally, since protection, the locally extinct rhinoceros auklet has begun to breed on the islands again. The island has the world's largest colonies of western gulls and ashy storm petrels, the latter species being considered endangered and a conservation priority. The island also is the wintering ground of several species of migrants, and regularly attracts vagrant birds (about 430 species of bird have been recorded on or around the island).
Five species of pinniped come to shore on the islands, and in some cases breed. These are the northern elephant seal, harbor seal, Steller's sea lion, California sea lion, and the northern fur seal (the last of which, like the rhinoceros auklet, began to return to the island again after protection).
Sealers took 150,000 northern fur seals (Callorhinus ursinus) from the Farallons between 1810 and 1813, followed by Russian fur hunters who lived on the Farallons and extirpated the pinnipeds from the islands. In 1996 West End Island became the fourth American northern fur seal rookery when a pup was born. The recolonizers bore tags from San Miguel Island in the Channel Islands, which had been itself recolonized in 1968. By 2006, nearly 100 pups were born. The fur seals are aggressive and have displaced larger sea lions from their territory. The high count for 2011 was 476 individuals, a 69 percent increase from the year before. By 2016, the pup count alone was 1,126, reflecting a 21% average (but highly variable) annual increase in new pups over the 21 years since recolonization. If the South Farallon Islands population reaches its estimated historical size of 100,000 individuals, it could account for approximately one-fifth of the world's northern fur seal population.
Northern elephant seals (Mirounga angustirostris) recolonized the refuge in 1959 with a confirmed pup in 1972. The elephant seal rookery on Southeast Farallon has probably reached carrying capacity.
Several species of cetaceans are found near the Farallon Islands, most frequently gray whales, blue whales, and humpback whales. Blue whales and humpback whales are most frequently found near the islands in the summer and fall, when strong upwelling may support a rich pelagic food web. Orca whales are also found around the islands. Gray whales are reliably found near the Farallones during their spring migration north and the fall and winter migration south. Some gray whales may also be found during the summer, when a few whales skip the trip north to Alaska and spend the summer months off the coast of Canada and the continental United States.
In December 2005 one humpback was rescued from netting entanglement east of the Farallones by staff of The Marine Mammal Center. The last sighting of another humpback, Humphrey, was near the Farallones in 1991. The islands are in the Gulf of the Farallones National Marine Sanctuary, which protects the feeding grounds of the wildlife of the refuge.
The elephant seal population attracts a population of great white sharks to the islands. In 1970 Farallon biologists witnessed their first shark attack, on a Steller's sea lion. During the next fifteen years, more than one hundred attacks on seals and sea lions were observed at close range. By the year 2000, biologists were logging almost eighty attacks in a single season.
While the males return annually, the females return only every other year, often with fresh, deep bites around their heads. The seasonal shark population at the Farallones is unclear, with estimates from thirty to one hundred. The Farallones are unique in the size of the great whites that are attracted. The average length of a full-grown great white shark is 4 to 4.8m, with a weight of 680 to 1,100kg, females generally being larger than males. Farallon great whites range between the "smaller" males at 13ft to the females, which generally range between 17 to 19ft. (For comparison, the largest accurately measured great white shark was a female caught in August 1988 at Prince Edward Island off the North Atlantic coast and measured 20.3ft.) A killer whale was recorded killing a great white near the Farallones in 1997. Over the decades of study, many of the individual white sharks visiting the Farallones have been nicknamed, often based on their scars and appearances, such as Gouge, The Hunchback, The Jester, and Stumpy. Stumpy, an 18-foot female great white, in particular was well known for her appearance in the BBC documentary "Great White Shark" narrated by David Attenborough and stock footage of her attacks on decoys is often utilized in more recent documentaries, and another example, Tom Johnson, a 16-foot male white shark that was featured in an episode of the 2012 season of Shark Week called "Great White Highway," is believed to be the oldest living white shark so far documented returning to the Farallones, estimated at around 25–30 years old.
Some individual sharks have been tagged and found to roam the Pacific as far as Hawaii and Guadalupe Island off Baja California, returning regularly to the Farallones every year in the autumn. Satellite tracking has revealed the majority of great white sharks from the Farallones (and from other parts of California, Hawaii and the west coast of Mexico) migrate to an area of ocean dubbed the White Shark Café, 1,500mi west of Ensenada, Baja California. The peak of activity at this location is from mid-April to Mid-July, but some sharks spend up to eight months of the year there. This island has many migratory sharks return to its waters every year.
The islands have tens of thousands of invasive house mice that are wreaking havoc on the native ecosystem. An average of 500 Eurasian house mice occupy each of its 120acres, with an approximate total population of 60,000.