Mugu Lagoon Losing Itself in Sediment : Environment: Salt marsh is being overrun by 240 million tons of silt annually carried by freshwater streams that threaten rare and endangered species. Report suggests remedies, but nature may have the solution.

VENTURA —  Steve Schwartz pauses on a cracking, concrete dock on the Point Mugu Navy base, surveying the rising salt marsh and dry land around him.

Sailors used to navigate 20-foot boats to the dock, puttering around Mugu Lagoon as recently as the 1960s. More recently, Schwartz and another Navy ecologist ventured here in a shallow-draft canoe. “We bottomed out,” he said.

About 240 million tons of sediment sweeps into Mugu Lagoon every year, depositing sandbars for lolling harbor seals and resting shorebirds where there was once deep water.

The grains of sand and silt are carried by runoff down a web of creeks and arroyos that reach into the hills above Simi Valley, Moorpark, Camarillo and Thousand Oaks.

A recent report on the 343-square-mile Calleguas Creek watershed says the accelerating flow of freshwater and sediment threatens the habitat for endangered and other rare species in Southern California’s largest remaining salt marsh.

The infusion of freshwater decreases salinity, killing some fish that require salt marsh conditions, the two-year study says. It also carries urban pollutants and pesticides from farmland.

The accompanying sediment is burying eelgrass beds that provide a nursery for fish, the report says, and is covering a delicate ecosystem under tons of mud and sand.

“With the loss of wetlands elsewhere, this area takes on an increasingly important role for migratory birds as a stopover on the Pacific Flyway,” said Sheri Klittich, a soil conservationist with the U.S. Department of Agriculture’s Natural Resources Conservation Service.

Mugu Lagoon also provides food and shelter to the endangered American peregrine falcon, the California least tern, light-footed clapper rail and the California brown pelican, the report said. In addition, it is one of the few remaining places in Southern California where harbor seals pup.

The report, written by Klittich’s co-workers with help from local, state and federal officials, suggests a variety of tactics to control farmland erosion.

It also recommends that county flood control officials build concrete and earthen structures to capture the sediment before it pours into the lagoon, including a major catch basin just upstream near Pacific Coast Highway.

The report acknowledges that it cannot determine exactly when Mugu Lagoon would be filled in, given the influence of ocean tides and other factors.

Yet it cites an earlier study that projected that most of the area will rise to five feet above sea level in about 40 years, shrinking the lagoon to a fraction of its size.

Schwartz, who helps lead a team of Navy biologists, is not so sure of the imminent doom of the wetlands. He sees another force of nature at play: A deep canyon in the ocean floor has started sucking away the Navy base’s shoreline like a huge sinkhole.

The 300-foot-deep marine canyon, which stretches miles off the coast, has started moving inland. It has gobbled up the 200-foot wide beach that used to protect the base’s old officers’ club and other facilities on a spit of sand between the ocean and Mugu Lagoon.

Navy crews have chopped off the end of the pier that slumped into the canyon. Now a huge rock seawall protecting Navy buildings has begun to slide into the submarine trench. Schwartz said the Navy plans to retreat from the advancing ocean, demolishing two buildings standing in its way.

Preliminary studies project that the canyon will continue to eat away at the sand spit until it connects with the lagoon within 20 to 40 years, Schwartz said. “When that happens, it could end the sediment problem,” he said.

The flow of silt and sand is as old as the Oxnard Plain itself. Sediment has washed down these creeks and nearby Santa Clara and Ventura rivers for eons, fanning out across the plain to deposit a rich layer of topsoil.

The river of sediment picked up speed during World War I, when farmers uprooted native vegetation on hillsides around Camarillo to make room for lima beans, the report said.

The Navy dredged the lagoon in 1946, but neither the report nor Navy officials suggest doing it again.

In addition to the disruption of wildlife, dredging could stir up DDT and other agricultural pesticides and pollutants that have poured into the lagoon.

“If you have a layer of DDT or heavy metals five feet down, you’d just mix it up in the water and expose endangered birds and species again,” Schwartz said. “Right now, it is more or less entombed.”

Without the option of dredging the lagoon, soil conservationists have focused on solutions upstream along the 36-mile-long Calleguas Creek, which has three different names.

It is called Arroyo Las Posas in its middle section and Arroyo Simi to the east, where it wends through Moorpark and Simi Valley. The creek’s tributaries include Conejo Creek, Arroyo Santa Rosa, Beardsley Wash/Revolon Slough and dozens of streams throughout the watershed that is 30 miles long and 14 miles wide.

The report released this month suggests giving the public better access to Mugu Lagoon, which can only be visited with special permission of the Navy.

“It has a real identity problem,” said Peter Brand of the state Coastal Conservancy, which provided a $100,000 grant to help with the $256,000 report.

Schwartz said the base’s environmental office is working on a plan to create a special gate onto the base for the public to visit the wetlands without needing to penetrate the shield of tight security.

Protected wetlands and salt marsh make up 2,500 of the base’s 4,490 acres, and much of the fragile area is separated from the buildings reserved for missile tests and other secret work.

“There are some peaceful spots out here,” Schwartz said, scanning the wetlands from the old boat dock. “You’d never know you were on a Navy base--until an F-14 screeches by.”