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Sand dredged from the San Joaquin River is pumped to the nearby Antioch Dunes National Wildlife Refuge in Antioch, Calif., on Thursday, Oct. 17, 2013. (Paul Burgarino/Bay Area News Group)

ANTIOCH -- A flurry of activity just off this city's shore this week may not only clear the way for Northern California commerce, but also could boost the population of a near-extinct native butterfly species nearby.

Workers with the U.S. Army Corps of Engineers and Oakland-based Vortex Marine Construction were dredging part of the San Joaquin River just east of Antioch's downtown Thursday -- annual maintenance done to clear the path for larger ships to bring cargo into the Central Valley.

The project is sponsored by the Port of Stockton, which provides information about which areas should be dredged. Making the shipping channels deeper allows bigger ships to move cargo between the Port of Oakland and Stockton.

"It's critical to our infrastructure," said Jeff Wingfield, the port's director of environmental and government affairs. "We need to keep that channel free so the ships can get in and out smoothly."

For the first time the sandy leftovers are being pumped to the nearby Antioch Dunes National Wildlife Refuge to help spur population growth for the Lange's metalmark butterfly. The dunes are the only place on the planet home to the bright reddish-orange breed of butterfly, which is on the brink of extinction.

"It's really a win-win for everybody," said Louis Terrazas, a wildlife refuge specialist with the U.S. Fish and Wildlife Service.

In past years, the Port of Stockton has placed the excavated sand on Sherman Island or worked with agencies to use it for levee restoration, Wingfield said.

This time the dredged material is being pumped to the Antioch refuge using a hydraulic cutter-suction dredger and through a fish screen. The sand is then moved to the refuge area and separated from the water as it flows into a series of berms. The water is then pumped back into the San Joaquin River.

Heavy machinery at the refuge was pushing the sand into large mounds Thursday. All told, it is anticipated that about 27,000 cubic yards of sand will be collected.

"It really is an exciting project to be a part of," Wingfield said.

Terrazas says his agency put out word a couple of years ago asking for a clean source of sand to restore the 41-acre part of the refuge near Fulton Shipyard, called the Stamm unit. They reached an agreement with the port that both sides say is beneficial, as the refuge gets free sand and the port is not charged tipping fees.

At one time, thousands of Lange's metalmarks lived in the area off the San Joaquin, but numbers dwindled early in the century as the growth of the Bay Area led to heavy sand mining and local industrial development.

The refuge was established in 1980 to help the butterfly, and endangered evening primrose and Contra Costa wallflower. It includes two areas, the Stamm and the 14-acre Sardis unit, which is near NRG and Pacific Gas & Electric's power plants.

The number of Lange's metalmark butterflies in the wild plummeted from 2,342 in 1999 to 45 in 2006. There were 78 this year, the most recent count done in August when the butterflies emerged from their chrysalises. However, none has been found on the Stamm site in three years, as the area has been prone to fires and invasive plants.

"It is no longer an active dune system, so we have to mimic the natural sand dunes," Terrazas said.

The dredging in the Antioch area should last another week. Terrazas hopes this becomes a long-term partnership.

The activity piqued the curiosity of some Antioch residents this week because of a floating contraption on the river and orange buoys. The mystery object on the river was extra pipe, Vortex officials said.

Once the sand is in place, Terrazas and his team will replant buckwheat and the two endangered plants, both adult plants and collected seeds and introduce butterflies to the area a year or two later.

"We're trying to get the site back in shape," Terrazas said. "There may be a learning curve, but hopefully the butterfly population will take off."

Contact Paul Burgarino at 925-779-7164. Follow him at Twitter.com/paulburgarino.