West Coast
Sparse grass pokes up through the water inside the decimated wetlands near Vallejo.Photo: Jessica Christian / The Chronicle

New maps show how little is left of West Coast estuaries

The most detailed study ever done of coastal estuaries concludes that nearly 750,000 acres of historic tidal wetlands along the West Coast, including enormous swaths of Bay Area habitat, have disappeared largely as a result of development.

The cutting-edge survey led by the National Oceanic and Atmospheric Administration determined that 85% of vegetated tidal lands that once existed in California, Oregon and Washington has been diked, drained or cut off from the sea.

The study, published Wednesday in the scientific journal PLOS One, documented dramatic decreases in wetland habitat around San Francisco Bay, the Sacramento-San Joaquin River Delta and nearly 450 other bays, lagoons, river deltas and coastal creek mouths throughout the West.

“We now have a new and considerably more accurate measure of the historical extent of these estuaries,” said Laura Brophy, director of the estuary technical group at the Oregon Institute for Applied Ecology and the lead author of the study. “Having accurate spacial mapping is important because many groups use these maps to locate restoration opportunities and to understand the impact we have had on the landscape.”

Scientists from eight government and environmental science laboratories used lasers that measure reflected light, known as Lidar, and compared the results with digital water elevation models kept by NOAA to map the contours and historic reach of the tidelands.

“No other region of the U.S. — in fact, no other state in the country — has fully mapped its estuaries using this method, which is far more accurate than past methods such as air-photo interpretation,” Brophy said. “Thus, the work is highly significant in itself.”

The estuaries in the three states once covered nearly 2 million acres, an area three times the size of Rhode Island, before humans began altering them in the 1800s. The lush tidal vegetation that is known to support birds and wildlife covered 877,792 acres. Only 131,818 acres of that verdant marshland is left, according to the study.

The researchers found that more tidal land disappeared from river deltas than anywhere else. That was particularly true along the Sacramento-San Joaquin, where 96.8% of the more than 380,000 acres of vegetated wetlands that once existed is gone.

Only about 15% of the historic marshland habitat around the main part of San Francisco Bay still exists, according to the study. That’s not surprising to wetlands restoration advocates, who have long used estimates of the bay’s historic marsh habitat that roughly conclude the same.

What’s new, Brophy said, is that the data break down each area of the bay and other estuaries in broader detail, allowing scientists to make comparisons and more easily calculate tidal action and what restoration techniques would work best as the sea level rises.

The study shows, for instance, that the South Bay suffered the biggest habitat losses over the years, with 86.2% of the wetlands disappearing. San Pablo Bay, the northern extension of the bay, lost 75.3% of its tidal vegetation over the years.

San Francisco Bay as a whole — including the South Bay, San Pablo Bay and Suisun Bay — lost 82.7% of the original 190,135 acres of tidal wetlands that existed before humans altered the shoreline.

Most of the other estuaries in California also lost ground, including Elkhorn Slough at Monterey Bay, where 69% of the original wetlands have disappeared. The most pristine estuary in the Bay Area is Drakes Estero in Marin County, where only 2.7% of the historic tidal habitat has vanished, according to the study.

Some places have actually been scoured almost completely clean, like Samish Bay in Washington state, where 98.2% of the historic wetlands are gone.

In addition to the hundreds of thousands of acres of marshland that were drained or diked off, the researchers discovered former wetlands that now are forested that were unknown to anybody. Brophy said this overlooked habitat could open new opportunities for restoration.

“By folding in these areas that may not have been recognized as part of estuaries,” she said, “we have a better idea of just how important and extensive these estuaries were.”

Brophy said the high-resolution maps also could be used to identify and fix low-lying areas most at risk for flooding in higher seas, which federal scientists calculate are rising at a rate of about an inch every six years because of global warming.

It’s important, conservationists say, because wetlands absorb high tides, can reduce flooding and provide important habitat for endangered fish, mammals, reptiles and shellfish. More than a million migrating birds visit the 400-mile San Francisco Bay shoreline every year.

Rivers, lagoons and marshes are critical nurseries for juvenile salmon and steelhead as they make the transition from freshwater to the ocean.

“Given how valuable estuaries are to so many different species, it’s important to understand how much they have changed and what that means for fish and wildlife that depend on them,” said Correigh Greene, a research biologist at NOAA Fisheries and a co-author of the study.

As the Trump administration relaxes rules protecting wetlands and streams, communities around the bay have already begun identifying areas where tidal marshes can be expanded, restored or re-created. A restoration blueprint, called the San Francisco Bay Shoreline Adaptation Atlas, was released in May by the San Francisco Estuary Institute and SPUR, a San Francisco urban planning research center.

Wetlands restoration has been going on for years in the former salt ponds in the South Bay and on former hay fields along Highway 37 in the North Bay. In North Richmond, the California Coastal Conservancy recently installed 350 reef structures and planted eelgrass to connect the wetlands to upland habitat. Work has also been done at Yosemite Slough, at Candlestick Point.

The goal is to eventually restore 100,000 acres of bay marsh, much of it in the Napa and Suisun areas, along the Petaluma River and in the South Bay.

“Now,” Brophy said, “we can see new restoration opportunities that people didn’t realize existed.”

Peter Fimrite is a San Francisco Chronicle staff writer. Email: pfimrite@sfchronicle.com. Twitter: @pfimrite