SAN JOSE — Claiming that mismanagement by Silicon Valley’s largest water agency has likely wiped out endangered steelhead trout in Coyote Creek, a coalition of environmentalists, including the Sierra Club, has filed a complaint with state water officials seeking to force big changes to protect the fish in the nearby Guadalupe River.

The groups contend that the Santa Clara Valley Water District has not released enough water from its dams into the creeks that feed the Guadalupe, the main river that flows through downtown San Jose. They also claim that a concrete barrier the district built on the upper river roughly 50 years ago near Almaden Expressway and Highway 85 to divert water to recharge underground aquifers is killing the fish.

“The trout are an indicator of stream health,” said Richard McMurtry, a board member of the Santa Clara County Creeks Coalition, which filed the complaint. “Basically, the water district is operating their facilities in a way that harms the health of the stream. We’ve been working with them on this for three years, and they’ve refused to do anything about it.”

The district provides drinking water and flood control for 1.9 million Santa Clara County residents. The environmental groups are asking the State Water Resources Control Board, which regulates water rights and water quality in California, to order the district to release more water every year from Guadalupe and Almaden reservoirs and to re-engineer the concrete barrier. Those actions potentially could result in less water available for people.

Water district officials would not immediately comment on the specifics of the complaint but defended the agency’s environmental record.

District leaders, “take stream stewardship seriously,” said CEO Norma Camacho, adding that the agency is “proud to be a staunch environmental advocate.”

In recent years, she said, the district has installed fish ladders, organized hundreds of cleanup events and provided grants to community organizations working to improve creeks across the South Bay.

“We work hard to enhance, protect and restore creeks and habitat,” she said.

The environmentalists, however, contend that although the agency’s staff has often been receptive to changes that would benefit endangered fish, its leaders often have not.

“Nothing ever happens,” said Katja Irvin, conservation committee co-chair of the Loma Prieta Chapter of the Sierra Club, based in Palo Alto. “The water district touts that they do stewardship, but it’s not something that they have done for very long and it’s subsidiary to water supply and flood control. They don’t really give it its due.”

“The bottom line,” she added, “is that they are going to have to give more water to the environment. The idea of giving up some water for a fish — the upper level management doesn’t make that a priority. They actively squash it.”

The groups say that water district officials release water at the wrong times of year and in the wrong amounts from Guadalupe and Almaden reservoirs, both located in south San Jose near Almaden Quicksilver County Park. As a result, sections of the creeks that feed the Guadalupe River dry out, killing endangered fish.

They are asking the state water board to declare that the operation of the reservoirs violates a provision in California’s constitution that prohibits the “unreasonable use” of water and to order the water district to draw up a plan in three months that sufficiently protects the fish.

The groups also are particularly incensed about a 13-foot-high concrete structure on the upper Guadalupe River. Known as the Alamitos Drop Structure, the facility is used in spring months to help recharge local aquifers. Water district officials erect a five-foot high wall on top of it called a flashboard, which backs up the creeks that feed the river, creating a temporary lake of about 500 to 700 yards long.

Water from that lake is then piped into a nearby percolation pond, where it seeps underground and recharges the aquifers that provide drinking water to the area. But the way the lake is created warms the water, the critics say. Young steelhead trout need cold water to thrive. And it creates a habitat for other fish, like bass, that eat the trout.

McMurtry said the district should re-engineer the system to divert the water from higher upstream and fill the percolation pond area from another nearby source, like Almaden Lake. That would cost roughly $3 million, he estimated.

“The district’s management doesn’t want to spend the money,” he said.

The environmentalists said they took action following a report earlier this year by Jerry Smith, an emeritus professor of biology at San Jose State University, that found no steelhead trout in nearby Coyote Creek in surveys over the past two years, despite the fact that they had been found in 2015 and in years before. That led to fears the fish may have been wiped out in that creek, a decline that Smith attributed to the recent drought and reduced water releases from the dams.

McMurtry estimated that about 5 to 10 percent more water would need to be let out of Almaden and Guadalupe reservoirs for the fish. Under the “public trust doctrine,” a legal concept that requires the government not to erode resources owned by all the public, such as wildlife, the water district must better balance the fish and public water needs, he said. Much of the water in the stream seeps eventually into the aquifers anyway, where it can be used by people, he added.

“The water district is making this such a low priority that they have wiped the steelhead trout out of Coyote Creek,” he said. “And we don’t want them to do it at the Guadalupe River.”