Rocks and Hazards to Know, Love, and Avoid on San Francisco Bay
By Patrick Twohy
San Francisco Bay is a challenging place to sail in many respects. Throughout most of the year, strong winds — more than 20 knots on a typical day — blow across our waters. We have tidal currents that can match the top speed through the water of some of our boats. And much of the bay is unmarked and too shallow to navigate safely.
One thing we don’t generally have to contend with in San Francisco Bay is a plethora of rocks or islands. Unlike in some sailing venues — the coast of Brittany comes to mind since I was there recently — we don’t face a maze of hidden hazards every time we leave our slip.
Which is not to say we don’t have such hazards. The fact that there are so few can lull a typical sailor into believing that there is nothing out there to fear, which would be a mistake. Plus, some of the bay’s rocks have interesting stories connected to them. And every skipper needs tales to yarn for their captive-audience crew, right? Just so.
So I’m here to help with a rundown of some of the Bay’s best rocks and rock stories.
Alcatraz: It’s The Rock, so let’s start there. But you already know all about it: Al Capone, Birdman of Alcatraz, a whole yard sale of movies on DVD. But do you know about Little Alcatraz? If you don’t, you need to. The rock thus familiarly christened is an outcropping often hiding under water just west of the northwest corner of Alcatraz. It is a hazard to navigation at any tide state.
NOAA Chart 18653 
Photo Credit Alcatraz – Patrick Twohy
It marked on charts of San Francisco Bay with a symbol that looks like an asterisk, indicating a rock awash at low tide. Note that the depth marked next to it is an underlined 5 — which means the rock rises 5 feet out of the water at mean lower low tide. To be safe when rounding Alcatraz, you must stay west of the Alcatraz junction buoy labeled GR “AZ” on charts. Don’t be the sailor who has to tell the Spinnaker office that Little Alcatraz left a gouge in your keel on your way around The Rock.
Berkeley Pier: In the days before bridges spanned the Bay, the route from the East Bay to San Francisco for many commuters involved a tram ride to the end of the a pier that ran from Berkeley two miles out into the Bay. There, passengers transferred to ferries for the rest of their ride into the city. The ferries went away soon after the Bay Bridge opened in 1939. After that, Key System trollies used the bridge to deposit riders directly at the transit center in San Francisco. (Until the late 1950s, the lower deck of the bridge was for rail and truck traffic while the upper deck carried autos going both directions.)
The pier was left to rot, and much of it was closed to the public. A short portion was refurbished and used as a fishing pier until that, too, was “temporarily” closed in 2018 as a deteriorating hazard. But the structures remain and can be a major hazard for unaware mariners. The end of the pier’s ruins are marked by a red channel marker (FL R 4s 15ft 4M “2”) Locals often use a navigable gap in the pier at the end of the old fishing pier portion of the structure to avoid having to go all the way around the pier when going from, say Berkeley Marina to the Oakland Estuary. It’s not marked on charts and it’s narrow, but usable. DON’T attempt to go through any other portion of the pier ruins or you could become part of the ruins yourself!
You may wonder why the ruins aren’t removed if they’re such a hazard. Part of the reason is the expense. But another is that over the years, the pilings have become a protected sanctuary for all sorts of marine and bird life.
Berkeley Reef: Speaking of Berkeley, you could plan a visit there by water to eat at Skates with its amazing view, or at Hana Japanese steakhouse, or at the Doubletree hotel’s restaurant Berkeley Boathouse, or at the famous Seabreeze cafe, built of shipping containers where University Avenue meets the Bayshore. If you do, please be aware of this reef just north of the harbor entrance.
I have nothing special to say about this hazard, other than that it’s going to be a surprise the first time you see it in what is otherwise wide open, safe sailing territory. There’s a lighted warning atop the reef that emits two green flashes every five seconds.
Southampton Shoal: If you were to then sail from Berkeley to Angel Island, aside from missing Berkeley Reef, you should also keep an eye peeled for the ruins of Southampton Shoal light. The shoal itself, 14 feet deep at mean lower low tide, isn’t a hazard for us. But what’s left from what was once a lighthouse marking the shoal is. (The lighthouse that once stood atop these ruins is still doing well — it was removed from the piers it was on in the 1960s and towed to Tinsley Island, the St. Francis Yacht Club’s retreat in the Sacramento River Delta, where the former lighthouse serves as luxury lodging, among other things.)
Southampton Shoals – USCG 
Tinsley Island – St. Francis Yacht Club
The pier ruin looks like a concrete box with legs. It is marked by a bell and a red light that cycles on for six seconds followed by six seconds off.
Brooks Island: This one isn’t so much a hazard as a curiosity. Brooks Island, which today forms part of the breakwater protecting the Port of Richmond, has been a lot of things over the years — shell mounds indicate active use by Native Americans. Since their days, the island has been grazing land for cattle and sheep, a sandstone quarry that purportedly provided some of the material to build San Quentin Prison, and a luxury hunting club with members the likes of Frank Sinatra and Bing Crosby. Today it’s a regional park, but don’t bother trying to book a visit. It’s closed to the public except by special arrangement. (I’m not saying who or when, but members of a club I know of occasionally sail dinghies or paddle kayaks there to look around.)
Red Rock: This one might be my favorite on this list, due to its mysterious nature. This 150-foot-high rock is the only privately owned island in San Francisco Bay. It is just south of the Richmond-San Rafael Bridge where it is the meeting point of borders of three Bay counties — San Francisco, Marin and Contra Costa. I have to assume that means doing any kind of development on the island, already terrifically difficult due to restrictions on work along the water, would have to be at least two or three times more difficult than any other development on the bay.
I’ve heard tell that Jack London, the San Francisco Bay-based writer who was a deeply committed sailor, used to row out to the island with his buddies and get drunk.
Like Brooks Island, Red Rock has been a hunting preserve and a mining site — manganese was what miners were after here. It was owned for a while by a guy who sold gems in Thailand. He listed it for sale in 2007 for $10 million. I heard a possibly apocryphal story that he won the island in a card game. Published stories say he actually bought it in 1964 for $49,000. I prefer the card-game story, of course. Anyway, it’s not entirely clear who the current owner is, or whether the island is still for sale.
Wooooo! Mystery!!
That isn’t the end of my list of hazardous mysteries on our glorious Bay. In a later installment, I’ll share tales of the South Tower Demon, the ship that gave its name to Blossom Rock, and sites around the region named for the ships that sank there — and whose ghosts probably still haunt the sites.