MercuryNews.com

Every day, millions of Northern Californians drive, fly and walk around San Francisco Bay. But most have no idea that nearly half the bay, from San Francisco International Airport to San Jose, is just six feet deep or shallower.

Large areas off Alviso, Fremont and Redwood City are no deeper than the shallow end of a children's pool. If it wasn't for the sinking mud, people could walk miles out into the water without it ever going over their heads.

For the past several months, a team of state and federal researchers has been assembling the most detailed study ever completed of the South Bay's underwater features -- all part of a project to develop 3-D maps and computer images of what lies beneath the body of water that gives the Bay Area its name.

Similar depth studies, a science known as bathymetry, have been completed five times since 1858, usually for navigational charts to help boats negotiate the bay's tricky depths.

But this project, by crews from the U.S. Geological Survey, is intended to go much further, measuring how millions of tons of mud and silt move across more than 30 miles of South Bay floor every year. The findings will be a critical part of the massive state and federal project to restore 15,100 acres of former Cargill industrial salt evaporation ponds that ring the shoreline from Hayward to Alviso to Redwood City back to healthy wetlands for wildlife and fish in the coming decades.

``Most obvious, over the last 150 years, there's been a loss of marshland, and a loss of tidal mud flats in the bay,'' said Bruce Jaffe, a research oceanographer with the USGS working on the project.

``But less obvious -- and the most important change in terms of salt pond restoration -- is that overall since the 1850s, the South Bay has lost sediment.''

To be exact, erosion from South San Francisco to San Jose has resulted in a loss of 90 million cubic meters of mud and sand from 1858 to 1983. That is the equivalent of 130 million dump truck loads that have flowed out through the Golden Gate into the Pacific Ocean.

Much of that erosion has been caused by natural forces such as waves, tides and storms. Some is the result of human activities, such as building dams, which block sediment from flowing down creeks into the bay.

Why does any of it matter to the salt ponds restoration?

The trouble is, many of the ponds in Alviso and other South Bay communities -- which were used to evaporate salt for roads, food and chemicals over the past century -- are up to four feet deep. To re-create a wetland, they can be no more than a few inches deep so that plants will grow.

Crews are scheduled in 2006 to begin breaching the earthen levees on three ponds off Fremont near the former community of Drawbridge, with large-scale breaching on other ponds to begin in 2008. Then, planners hope that sand and mud will be carried in from bay currents to help raise the bottoms of the deeper ponds so plants such as bull rushes and pickleweed can grow, providing habitat for fish and birds.

``Dirt, plants and animals -- in that order. That's restoration,'' said Amy Hutzel, project manager with the California Coastal Conservancy in Oakland.

The Coastal Conservancy will spend roughly $600,000 on the mapping project of the South Bay, Hutzel said.

The money has funded three key kinds of study. First, last May, it paid for an airplane to fly for two weeks over the bay, using a system called LIDAR that bounces laser beams off the ground to measure precise features of the South Bay's marshes and tidal mud flats. Second, it paid for the USGS to take more than 100 sediment samples in the bay and study them for age, using geologic dating techniques; grain size (small grains move more easily in water); and contamination, because there is some concern that old, buried pollutants such as lead, mercury or DDT might be uncovered by large-scale movements of sand and mud.

All the data will be crunched, and preliminary maps are expected by this fall, with final images done next year.

``This is by far the most comprehensive look at South San Francisco Bay that has ever been done,'' Hutzel said. ``It's exciting. You'll be able to see movies showing what the South Bay would look like if you were flying over in a plane and it had no water.''

In the first South Bay survey, done in 1858, seven men spent five years in a rowboat, dropping a lead weight on a rope and recording locations with a sextant.

Last week, a crew from Sea Surveyor, a Benicia firm, worked from a 29-foot boat named the Minotaur. Aboard were laptops with global positioning systems, radar, depth sounders, sonar, cell phones, weather radios and a space heater.

``Those guys 150 years ago spent five years throwing out that lead line over and over again thousands of times,'' said Steve Sullivan, vice president of operations for Sea Surveyor, as the boat bobbed south of the San Mateo Bridge.

``It will take us two months to do the same thing. Things have gotten a lot better.''

There are still many questions left unanswered. Although the South Bay lost sediment overall between the first survey in 1858 and the most recent one in 1983, there have been periods when it had a net gain, such as in the late 1800s, when hydraulic mining in the Sierra sent billions of pounds of mud flowing into the bay.

Luckily for the state and federal agencies working on the salt pond restoration, the southernmost portion of the bay, near Alviso, where the salt ponds are deepest, has consistently silted up over time. A lack of heavy tidal action is believed to be the cause. That means even if the bay is in a period of net erosion, it may still be possible to increase the elevations of the deepest ponds so they can be restored to wetlands.

The seemingly mundane study of mud couldn't be more important to the bay's restoration, said Lynne Trulio, dean of San Jose State's environmental studies department.

Trulio said mud ``is the driver for restoring wetlands. We need to know how much is out here so we can learn how much of the salt ponds can be restored. Mud is central to that whole effort.''