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History Written in Water

We profaned the bay, then tried to save it. Now we’re learning that it has a mind of its own.

The San Francisco waterfront around the turn of the nineteenth century.

The San Francisco waterfront around the turn of the nineteenth century.

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The San Francisco waterfront around the turn of the nineteenth century.

A swimmer from the South End Rowing Club (established 1873) heads for the Farallon Islands, 28 miles offshore. (2 of 5)

The San Francisco waterfront around the turn of the nineteenth century.

A derelict structure at Pier 70. (3 of 5)

The San Francisco waterfront around the turn of the nineteenth century.

Bundled-up beach-goers below the Cliff House, 1902. (4 of 5)

The San Francisco waterfront around the turn of the nineteenth century.

Less formally attired plungers brave chilly Ocean Beach waters on the 2012 winter solstice.

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San Francisco Bay is clearer than it has been since the gold rush. Its waters are less muddy, and much of the befouling sediment that formerly covered the bay floor has washed away into the Pacific.

Good news, right? Wrong. Actually, the fact that the bay’s water is more transparent than it has been in 150 years is causing some serious problems, a development that is both unexpected and deeply ironic. The silt that until recently muddied the bay was created by what has always, and rightly, been considered California’s first and worst environmental disaster: hydraulic mining. By 1853, panning for gold was no longer profitable, so miners began using water cannons to blast away riverbanks and entire mountains. The amount of sand and dirt blown loose was inconceivable: One geologist estimated it at one and a half billion cubic yards, or eight times more than the material removed to build the 48-mile-long Panama Canal. So vast was the quantity of sediment that the mighty Sacramento River’s bed was raised 13 feet at the capital.

Enormous quantities of fine-grained sediments, called “slickens,” were washed into San Francisco Bay, leaving 272 square miles of our backyard estuary eight inches shallower. This ocean of ooze radically altered the bay, wiping out some bottom-dwelling species and, worst of all, leaving behind toxic deposits of mercury.

Today, the great mudslide that clogged the estuary for a century and a half has been mostly washed out to sea by tidal action. You’d think that this would be cause for rejoicing: Nature, in its wisdom, has rectified a man-made environmental disaster. But the story, like most having to do with the great, unknowable body of water that defines our region, turns out to be more complicated than that. Far from benefiting the built environment of San Francisco and the Bay Area, the loss of sediment that has brought us a cleaner, clearer bay is also causing our home to be slowly swallowed by the sea.

For the next several weeks, San Francisco will be publishing stories that examine our evolving relationship with the waters lapping our shores—be they the bay, the Pacific, the delta, or the hidden springs beneath our feet. Online at and in the pages of our April 2013 issue, you'll find dozens of stories that shed light on  crucial issues pertaining to the waterfront: how we interact with it, how we manipulate it, and, most of all, how we fight over it.

It’s this last point that’s perhaps most salient. Conflict over the Bay Area’s waterways—who owns them, who should have access to them, what should be done with them—started with the gold rush and has never stopped. And though it’s sometimes hard, even at a distance, to discern the victor in these conflicts, one thing is certain: Their consequences can be unpredictable.

San Francisco Bay is only 10,000 years old, a mere faucet drip in geologic time. It was created at the end of the last ice age, when melting glaciers caused sea levels to rise. Yet this geological infant is one of the planet’s marvels. From its dark abyss under the Golden Gate, scoured by ferocious currents to a depth of 330 feet, to the tepid, lagoon-like reaches of the south bay, to the ambiguous, oddly far-inland delta, the bay is a unique natural system, one so complex that scientists are still trying to understand it. It is home to 120 species of fish, 1,000 to 2,000 sea lions, 600 harbor seals, and countless migratory birds drawn to its incredibly food-rich margins (marshlands generate more plant life per square foot than almost any other terrain on earth). Above all, it is an estuary—a place where freshwater and saltwater meet in an alchemical encounter. By definition, it is a place of ceaseless change, of recombination, of productive chaos.

Long before Central Valley farmers and city dwellers rose up in outrage over hydraulic mining, San Franciscans were squabbling not just over who owned the waterfront, but about its very existence— where it should be and who should be allowed to create it. Real estate, then as now, was fiercely fought over (sometimes, as during the Mission Bay tidelands dispute of 1867–1869, with cannon-armed gunboats), and the most valuable properties in the instant city were “water lots,” aquatic rectangles sold at sky-high prices because they would soon be solid land.

Nothing has changed. Waterfront property is still gold, and any proposed development on the San Francisco waterfront is still regarded with the enthusiasm the Taliban feels for a revision of the Koran. The latest example: former mayor Art Agnos’s passionate, populist-tinged crusade to enforce strict height limits along the waterfront. In a wide-ranging interview, Agnos tells editor-in-chief Jon Steinberg why this issue means so much to him.

It's a story with obvious antecedents. Land was more valuable than water in the city’s early days, and no preservationist ethos checked the frenzy to fill in the bay. San Franciscans dumped anything they could get their hands on into the water—quarried rock from Telegraph Hill, sand excavated from the great dunes that blocked Market Street, and the abandoned ships that filled Yerba Buena cove, today’s financial district. One old Norwegian sea captain specialized in surreptitiously scuttling ships on water lots, a lucrative but highly dangerous livelihood: The water lots were invariably located next to wharves whose bosses, understandably, did not want their piers to become uselessly landlocked—and they appealed to the court of Colt .31 to protect their property. Their efforts were futile: Forty-seven known gold rush–era ships, at least four of them scuttled under duress, lie buried beneath San Francisco streets that used to be piers.

At the same time that San Franciscans were relentlessly filling in the bay, they were doing the same thing to the city’s tidelands, marshes, and swamps, which once covered most of South of Market and extended inland almost as far as Mission Dolores. But they paid a high price for attempting to impose their will on the waters and wetlands. When the 1906 earthquake struck, it was reclaimed land, so-called “made ground,” that was hit hardest. Hundreds of people died in four cheap South of Market boardinghouses built on land that had once been a marshy pond named Pioche’s Lake. Another hundred died in the collapse of the Valencia Hotel, which stood atop an old branch of Mission Creek. Like Freudian repressed emotions, the buried waters exacted their toll.

Nature’s act of revenge did not change the attitude of San Franciscans toward the bay. They continued to regard it as infinitely resilient, something to be used and, if necessary, used up—a response that revealed the newly industrialized society’s schizoid attitude, at once worshipful and callous, toward the natural world. But if the concept of ecology was foreign to the people of the 19th and early 20th centuries, their actual lives were far more engaged with the bay than most people’s lives are today. Until well after World War II, for example, significant numbers of residents still caught or harvested food from the bay—a tradition that goes back more than 3,000 years to the Ohlone people, who left behind massive shellmounds as tangible evidence. (In a inadvertently ironic commentary, the site of the largest Bay Area shellmound, in Emeryville, was occupied for decades by a Sherwin-Williams paint factory with an enormous neon sign that showed a bucket of paint spilling over a globe, followed by the words “We Cover the Earth.”) The estuary was home to a prolific and lucrative oyster industry until the early 1920s, when pollution, shoreline fill, and fears of food poisoning devastated both supply and demand.

But for most of its history, San Francisco Bay served its city as one thing above all: a working port. There’s a reason why Mark Twain, in his classic story “Captain Stormfield’s Visit to Heaven,” has the old salt who tells the tale hail from San Francisco. As historian Michael Corbett points out, “If any city might justifiably have been called Port City, it was San Francisco for its first hundred years. The port did not grow so much to serve the city as the other way around.” Shipping was the city’s lifeblood, a fact reflected in the longtime name for the Embarcadero: the City Front. The Ferry Building was San Francisco’s front door: In 1913, 60,000 commuters rode ferries into the city each day. The monopolistic railroads that dominated California’s economy for decades sprang up in San Francisco because of its port. From the Union Iron Works on Pier 70, which began building steel ships in 1882, to the stacks of copra (dried coconut meat) at Pier 84, San Francisco’s waterfront was a buzzing hive of activity. As recently as 1961, it was estimated that one-third of all workers in the city made some or all of their living from the port.

The end of this muscular era was presaged in 1958, when the first container ship sailed through the Golden Gate. Unable to compete with Oakland and other ports with more land, San Francisco’s working waterfront slowly died, replaced by a crazy quilt of uses. Where longshoremen once unloaded cargo, tourist- and consumer-oriented attractions like Fisherman’s Wharf, Pier 39, and the Ferry Plaza Farmers Market now stand. A magnificent public promenade has taken the place of the old Embarcadero, along which the state-owned Belt Line Railroad once carried goods from Singapore and Liverpool. And the long gray finger piers at which the ships of the world once tied up now house nonprofits and tech firms.

Page two: the never-to-be-solved mysteries of the bay