See whales, seals, birds, sharks during challenging boat excursion from San Francisco.

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SAN FRANCISCO — Just outside the Golden Gate Bridge in San Francisco Bay, we followed the footprints of a whale.

The footprints were real: flat slicks on the surface of the ocean formed when a whale’s flukes — the two lobes of its tail fin — push up water on a dive. Seabirds clustered above the same patch of water, interested in the fishy breakfast being stirred up there.

On this gray, drizzly morning, three adult humpbacks lazily circled our whale-watching vessel and dived down repeatedly to feed in the burbling waters where the bay meets the Pacific Ocean. We had barely begun our trip out to the Farallon Islands, 26 miles west of San Francisco, but we had plenty of company. Ten minutes later, out in the shipping lane five miles offshore, we came upon four more humpbacks. A gaggle of inert sea lions sat atop one bobbing green buoy, watching us go by.

If you go

Farallon Islands whale-watching and natural-history tours are offered by San Francisco Whale Tours (sanfranciscowhaletours.com; $80-$99 for six hours) on weekends only, year-round. June through November: Expect blue whales and humpback whales. December through May: See gray whales and sperm whales.

San Francisco these days doesn’t feel so wild to me, but then I step off its shores and head out into the bay. I think about how stunning it must have been when explorers first arrived at its mouth. People commute mindlessly over the Golden Gate Bridge day after day without realizing that whales, sea lions, seals and harbor porpoises congregate here still. Venture a little farther out from shore, to the Farallon Islands, and you get a sense of what it was like to truly feel wild, remote, at sea.

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Remoteness. Isn’t that what visiting a speck of land divorced from a larger speck of land is all about?

The devil’s teeth

Named for the Spanish farallón, meaning a rocky pillar jutting from the sea, the Farallones were called “the Devil’s teeth” by sailors in the 1850s for their ragged profile and treacherous shores, the cause of many a shipwreck. Today, the string of four groups of small islands totaling 211 acres is a national wildlife refuge, home to the largest colony of nesting seabirds in the contiguous United States. Five species of marine mammals all breed or haul out here, and great white sharks visit regularly to feed on many of them.

Though officially part of the city and county of San Francisco, the outcrops are uninhabited except for Southeast Farallon Island, where a handful of conservation scientists have a field research station. Permits to go ashore are rarely granted.

Although the Farallones are closed to the public, wildlife-viewing boats such as the one run by San Francisco Whale Tours can approach them with care. Our captain that day was Joe Nazar, and our naturalist was Steve Wood, a cheerful biologist who conducts research on marine invertebrates at Dominican University of California.

A word of warning: This is not exactly a pleasure cruise. Going out to the Farallones can be a challenging expedition. “Come dressed for the moon,” the trip material told us. It’s good advice. I dressed for the moon in fleece and rain layers and I was still cold. The air temperature topped out at 55 degrees, but the wind, rain and sea spray from the vessel’s wake chilled to the bone.

Although the boat has a covered cabin with booth seating that recalls the interior of a cozy diner, it is not where you want to be when the boat is ricocheting off 8-foot swells on the open ocean. About halfway to the islands, one young woman came lurching out of the cabin, eyes wild. She headed for the railing and threw up off the starboard side of the boat.

A wild world

Wood told us that sea lions, northern elephant seals, tufted puffins and other species had established zones on Southeast Farallon; as we cruised the shoreline, we got a closer look at a few of those neighborhoods. On one slope was an elephant seal rookery, with 500-pound juveniles lolling on the rocks. There weren’t any 2-ton adult males around that day (they can grow to the size of a pickup), but we could imagine. One juvenile can feed a great white shark for up to a month.

More than 400 species of birds have been recorded in the Farallones. We saw double-crested cormorants, red-necked phalaropes and common murres, which can dive hundreds of feet underwater to catch fish. That day the soundtrack to the islands was the cacophony of thousands of murres roosting together, which pretty much drowned out the songs of all other seabirds, save for the occasional gull squawk.

Later, on our way back through the Golden Gate, we had the most intimate encounter yet with the humpbacks, which seemed to be performing for us as they rolled and flipped their flukes. Suddenly an awful smell washed over the boat. Our marine biologist laughed when he told us that it was nothing more than the stinky baleen breath of a whale.