SAN JOSE — A $9.6 million plan to widen the lower Guadalupe River in Alviso, providing more access to boaters by removing thick sediment, bulrushes and tule reeds, has hit a possibly fatal setback, with federal officials denying it necessary permits.

The Santa Clara Valley Water District, a government agency based in San Jose, approved the project in 2009. The goal was to restore much of the lower Guadalupe River on San Jose’s northern edges, near where it empties into San Francisco Bay. If successful, the river would be brought back to conditions not seen since the early 1980s, before flood control work and other manmade changes caused the river to silt up and narrow.

The project calls for dredging the river to a depth of 16 feet and removing tidal marsh over a 4.5-acre area between the Gold Street Bridge and Alviso Marina County Park. Supporters include many of the 3,000 residents of Alviso, which was annexed into San Jose in 1968.

“I was born here in 1944. I used to swim there. We loved it,” said Dick Santos, an Alviso resident and member of the water district board. “I would see sea lions there eating herring and shrimp. Sturgeon, striped bass were there. They aren’t there now because everything changed to muddy freshwater. It should be salt water from the bay. It’s terrible. It’s an environmental injustice.”

In January, the Army Corps of Engineers’ office in San Francisco sent a letter to water district officials announcing that neither they nor the U.S. Environmental Protection Agency will issue permits for the job. The Army Corps said that the project is not the least environmentally damaging alternative, a standard required by the federal Clean Water Act.

There are other available sites for recreational boating marinas in the South Bay, the Corps said, including along the southern edge of Cargill Salt’s Redwood City property and at Westpoint Marina Harbor, also in Redwood City.

“There are a lot of problems with this project. There are endangered species. There is mercury contamination. They don’t have any state approvals,” said Mark D’Avignon, an Army Corps project manager in San Francisco.

Human alterations

A number of endangered species live in the area, including the salt marsh harvest mouse, green sturgeon, steelhead and the clapper rail, a diminutive bird. One fear is that by digging up large amounts of material in the channel, it would release mercury that has been trapped in the mud and sand for decades, having washed down the Guadalupe River from the old New Almaden Quicksilver mines in the hills south of San Jose. The mines closed 40 years ago, but when it rains, there is still mercury that runs down the river.

Santos and water district officials note that the river has been heavily altered by human activities, and that their project is not so much about boating as restoring the river to its original state.

“Obviously we are very disappointed,” said Ngoc Nguyen, an engineering unit manager with the water district. “We have had full support from the Alviso community for this project from Day One.”

The river’s woes took decades to unfold. Founded in 1852, Alviso began as a busy port. Steamships carried redwood, quicksilver and orchard fruits to the bay and around the world. But during the 1860s, when railroads were built between San Jose and San Francisco, they bypassed Alviso and eventually the port silted in.

The construction of salt evaporation ponds around the South Bay in the 1930s rerouted the Guadalupe River, cutting off tidal action. Later, in the 1960s, as Alviso was being annexed into San Jose, the Army Corps of Engineers and the water district straightened the river to improve flood safety. But in removing its lazy meanders, they inadvertently created a freeway for sediment, which now collects at Alviso.

Eight tidal gates

Photographs bear out the changes. In 1977, one spot in the river at Alviso was 218 feet wide. By 2004, it was 54 feet wide.

Santos and others contend that if the silt and overgrown vegetation can be removed, and saltwater from the bay reintroduced, more wildlife, recreational boaters and commercial fishermen will return.

They have asked the Army Corps to tell them how to redesign the project. That could take years, however. In the meantime, another project that the district and the U.S. Fish and Wildlife Service finished in 2011 may offer one option.

Under that project, crews cut a 40-foot channel between the river and Pond A-8, a former commercial salt evaporation pond. Eight tidal gates were installed. So far three have been opened, allowing some salt water from the bay to come into the river.

Eric Mruz, manager of the Don Edwards San Francisco Bay National Wildlife Refuge, said Sunday that he plans to open five gates this summer, after studies of mercury impacts on fish and birds are finished, with all eight gates opened by 2016. If everything goes well, he said, the salt water will kill much of the vegetation, and begin washing away the sediment. But getting the river back to its pre-1980s state could take decades.

“I’m 70,” Santos said. “I’d like to see it come back in my lifetime. You just have to have hope.”

Paul Rogers covers resources and environmental issues. Contact him at 408-920-5045. Follow him at Twitter.com/PaulRogersSJMN.