The deep secrets of S.F. Bay / Stunning 3-D underwater maps reveal surprises

On a bright spring day, San Francisco Bay may look like a placid blue lagoon, but it's a different story down below.

The bay, an estuary marked by complex movements of fresh and salt water, has long been a muddy mystery below the surface, shaped and reshaped by 150 years of human activity and by tons of sediment flushed in from the delta and drifting around with the strong currents.

Now, the U.S. Geological Survey has opened a new window on the bay beneath the waves in a stunning set of underwater maps. They are part of a 30- page report by geologist John Chin and colleagues documenting how nature and humans have transformed the floor of the central bay.

Even in two dimensions on a computer screen, the report offers a radically different view of the bay. Although not as conventionally pretty as the view you may be used to seeing, the maps make a complicated and fascinating portrait of the bay on its own terms.

"We've never had anything like this before," Chin said, crediting a decade of computer-aided mapmaking at the USGS.

The results are a revelation, even for some experts who have been studying the bay for decades.

"There's a lot more relief and perspective than what most people might think you'd find," Chin said. "Most people think of the seafloor and the bay floor as flat -- just mud, sand and very little else. But you see a lot of rocks, rock mounds, sand waves, deep holes and depressions, too."

All told, the estuary known as San Francisco Bay and the adjoining Sacramento-San Joaquin River Delta system cover 1,600 square miles and drain about 40 percent of California. The report focuses on the marks left on the bay floor in the modern era of population growth and industrial activity.

Much of what people have done in this vast watershed has had an effect on the bay's bottom, including an estimated 1.4 billion cubic yards of hydraulic mining debris -- eight times the amount of material carved out for the Panama Canal -- washed down from the Sierra foothills in Gold Rush days.

The sediments elevated native mudflats by as much as 3.3 feet in Suisun Bay, the report notes, altering tidal circulation patterns throughout the system and leaving permanent "legacy deposits" of mercury-laden sediment, still a problem in some areas anytime something disturbs the bay bottom.

People also have reshaped the bay floor in more direct ways.

Nineteenth century settlers confronted native bedrock knobs jutting up to just a few feet below the surface. The rounded peaks were simply blasted away to depths thought safe for the ships of the time. But remnants have become hazards once again to modern, deep-draft container vessels -- and a potential source of an oil spill should one happen to rip out the hull of a tanker.

Bar pilots, who steer the biggest ships inside the Golden Gate, know the locations of these rocks as well as commuters know the exit names and lane changes needed to make it over the Bay Bridge. The named rocks -- Shag, Arch, Blossom and Harding -- are shown on the new map roughly in line with Alcatraz, the classic "Rock" and the only one most people have ever heard of.

All are part of what is thought to be the same submerged, primordial mountain ridge. Discussions continue about the possibility of taking out the rock stumps once and for all, but so far experts judge it's better for pilots to steer clear of them, rather than undertake the expense and environmental disruption to remove them. Such informed debates are a fairly recent innovation, as the new report makes clear.

The aptly named Arch Rock, for instance, once stuck out of the water at low tide like the eye of a giant stone needle, presenting a portal through which boaters sometimes tried to slip for sport, with occasionally disastrous results.

It was blasted to smithereens in 1901. A rare sketch of the intact Arch Rock, and a photo of the dynamiting, are included in the new report.

The new picture of the bay bottom was drawn from high-resolution "multibeam mapping," in which a transducer on a ship sends out three pulses of sound per second. Detailed images are assembled from the acoustic backscatter picked up from the bay floor and any other solid surfaces the sound waves encounter.

By mounting the device to a ship's hull, rather than towing it in the wake as is typically done, scientists could cover more territory and were able to precisely knit together adjoining pictures.

Despite the high-tech sheen, however, the report barely scratches the subsurface. It covers only the west-central bay, a small area bounded roughly by the Golden Gate to just west of Treasure Island and the Richmond shoreline, extending from the top of San Francisco up and around Angel Island to the Tiburon peninsula.

Even so, David Lewis, executive director of the Oakland environmental group Save the Bay, called it "the most detailed picture I've seen of what's beneath the bay." It reveals in startling clarity "a highly altered environment," he said, "just like the parts of the bay and shoreline we can see are highly altered."

Until people began to realize its value, the bay was just a dump -- a bathtub with a clogged drain -- or real estate waiting to be filled in. That mind-set clearly shows to this day.

"We've dredged huge amounts of sand and sediment for landfill and construction projects. We've dumped huge amounts of material off Alcatraz and other places. We've dug out shipping channels and deepened harbors. We've blown up rocks. The shape of the bottom has changed, the depth of the water has changed," Lewis said.

There is still a lot of uncertainty about the real impact of all those changes on the life of the bay, and, perhaps most important, what can be done in the future to protect, or possibly even improve, critical habitats.

Scientists and bay preservationists said the real value of the new underwater bay view is its suggestion of a new way of thinking about the bay in three dimensions, rather than just fragile shoreline around a flat water surface.

"This mapping is a tremendous aid for our understanding of how dynamic the estuary is," said hydrologist Philip Williams, principal of a San Francisco consulting firm, Philip Williams and Associates, that is helping to devise plans for restoring some of the bay's intertidal wetlands.

"Suddenly the bay has been made transparent," he said. "You can look down and see how the sediment is moving, how the bay is evolving. Those are the really critical issues in the habitat restoration work going on right now. We have to think about the bay as a dynamic evolving landscape."

The economic lifeblood of the bay also depends on this. Historically, an estimated 2 inches of sediment builds up every year in the bay, more or less depending on location -- a huge problem for the shipping industry.

The bay mud was dumped off Alcatraz, under the assumption that the tides would carry it out past the Golden Gate. Out of sight, out of mind, was about as sophisticated as the environmental planning got.

The new map reveals in startling fashion how much bay mud just stayed where it was deposited, filling in what was once a deep depression in the bay floor, a captive pile just beyond the gates of the world's most famous prison island.

"We have been building mountains in the bay," said Will Travis, head of the Bay Conservation and Development Commission.

Meanwhile, the vast salt ponds of the South Bay, among other wetland areas, have sunk after being walled off so long from the tides. Their future depends on being built back up, presumably by redepositing tons of sediment scooped up from somewhere else. So the mud has suddenly become a valued commodity.

But environmental planners know they must take into account the bay's natural hydrology, and keep in mind the risk of causing new water pollution by disturbing the mercury and other mining deposits in the name of wetland restoration.

Jim McGrath, an environmental manager at the Port of Oakland, said the latest underwater soundings and USGS mapping of the bay floor comprise "some of the most important work being done for the future health of the bay."

Next month, it will also be available in printed form, complete with a big foldout map and 3-D glasses. To order the printed version, go to www.usgs.gov/pubprod/ and request USGS Circular 1259.