The mouth of the San Elijo Lagoon, where a $120 million restoration was completed three years ago, is filling with sand faster than ever, a condition that endangers the wildlife there.

Last week’s warm temperatures turned areas of the closed lagoon hypoxic for the first time this year, said Jennifer Bright, chief operations officer and philanthropy director for the Nature Collective.

That means fish, mostly small anchovies, began dying because of the low oxygen levels in the stagnant water, Bright said Monday.

Fortunately, the weather turned cooler this week. The die-off slowed or stopped, and shore birds quickly cleaned up most of the evidence. Still, the winter rains that naturally restore the lagoon are months away.

The lagoon’s outlet usually is bulldozed open once each summer, Bright said. This year it’s been done twice, and it’s needed again. The first time waves took a few weeks to refill the opening with sand. The second time it took just days.

The restoration, a project 20 years in the making, widened and deepened the lagoon channel to expand and improve the wetlands habitat. A healthy and biodiverse wetlands supports hundreds of important species of plants, fish and birds that help to keep a balanced ecosystem.

“We saw a lot of success with that,” Bright said.

Eelgrass thrives in the shallow water, where the plant provides a nursery for fish. Endangered species of native birds, such as the California least tern, feast on the fish and build their nests on the shore.

“By widening the channel (in the restoration), we get three times as much tidal flow into the lagoon,” Bright said. “But what it’s also doing is bringing more sand in.”

The sand is carried farther into the lagoon than in the past, reaching the channel beneath the railroad bridge between Coast Highway 101 and Interstate 5.

The Nature Collective, formerly known as the San Elijo Lagoon Conservancy, has overseen the care and preservation of the lagoon for nearly 40 years.

Almost every year the nonprofit uses bulldozers, skip loaders and trucks to open the lagoon after the summer waves build up a berm on the beach, closing the connection to the ocean.

“We knew we would still have to continue opening the inlet,” Bright said. However, the maintenance has become more than expected.

Now, in addition to another beach opening, the lagoon’s caretakers need to dredge the sand that has accumulated at the railroad bridge, an area that is harder to reach. That will require more money and heavy equipment, and probably a boat-based dredge.

A rough estimate of the work needed is $1 million, Bright said. The Nature Collective has issued a request for proposals that will help determine the cost, but so far it does not have all the money. Mitigation funds could be available from Caltrans or the San Diego Association of Governments. The lagoon restoration was paid for by Transnet, the half-cent sales tax approved by voters and administered by SANDAG.

Every year, sand from the opening is used to widen nearby beaches. During the restoration, thousands of additional cubic yards of sand dredged from the lagoon were used to expand more than half a mile of the shoreline at Cardiff State Beach.

Called the Cardiff Living Shoreline project, the sand was placed atop a buried rock revetment and planted with native vegetation to help protect Coast Highway 101 from the steady erosion of high tides and winter storms.

All of San Diego County’s coastal lagoons would naturally close up each summer without human intervention. Some, like Agua Hedionda and Batiquitos in Carlsbad, have been modified with rock jetties and periodic dredging to stay open year round.

Sand from those projects also is placed on nearby beaches to slow the effects of coastal erosion. A number of additional local and regional replenishment projects have been completed and more are planned to dredge offshore sand and place it on the shrinking shoreline.

All that sand placement also could be affecting the lagoons, filling them up faster, but the process is complicated and more studies are needed.

California’s wetlands were once considered wastelands, only fit to be drained, filled and developed. More than 90 percent of the state’s coastal wetlands have disappeared over the last century.

Only recently have people realized the value of their special coastal habitats and passed laws to protect them.