Restoration of Alameda Creek in the East Bay reached a milestone this spring when what appeared to be hundreds of steelhead trout hatched in a tributary to the creek. If the young fish are indeed steelhead — experts should know soon — they would mark the first natural reproduction of steelhead in the creek since the 1960s.

While the return of steelhead to Alameda Creek's lower reaches is being celebrated as a success story, the battle over how to manage the creek for the rare fish is ongoing. The coming fight is over the San Francisco Public Utility Commission's rebuilding of Calaveras Dam, which holds back waters feeding the upper portion of Alameda Creek and its tributary Calaveras Creek. Environmentalists and, recently, the National Marine Fisheries Service, insist the SFPUC must construct and operate the dam in a way that aids steelhead. Thus far, the SFPUC and the Army Corps of Engineers have declined to consider steelhead as part of the dam reconstruction project.

Still, Alameda Creek has come a long ways during the past decade. Four small dams have been removed, fish screens have been installed at diversion points, and habitat at the mouth of the creek in San Francisco Bay has been upgraded. And more restoration projects are on the way.

"We're looking at getting steelhead into Sunol Valley by 2012," said Jeff Miller, who heads the Alameda Creek Alliance. That would mean the rare fish could navigate more than 20 miles of waterway that for decades was inhospitable.

At about 670 square miles, the Alameda Creek watershed is the third largest in the Bay Area and includes portions of Alameda and Santa Clara counties. Historically, the creek and its tributaries supported anadromous fish such as steelhead and salmon that reproduce in freshwater but spend most of their adult lives in the ocean. Since the 19th century, however, Alameda Creek has been managed in a fashion detrimental to the fish. Dams were erected to create reservoirs and diversions were installed to provide municipal water supplies. After flooding during the 1950s, the Army Corps built a sterile channel for the lower 12 miles of Alameda Creek through Fremont and Newark. During the 1970s, a 9-foot-high cement weir was built to protect a BART line. And for many years, salt production ponds on the edge of the bay eliminated wetlands habitat.

By the 1970s, wildlife officials had essentially given up on steelhead and salmon in Alameda Creek. But things began to change — albeit slowly — when the U.S. Fish and Wildlife Service listed the Central California Coast steelhead as a threatened species under the Endangered Species Act in 1997. That year, environmentalists formed Alameda Creek Alliance, which succeeded an earlier group that had called it quits.

The biggest player in the Alameda Creek watershed is the San Francisco PUC, which diverts most of the flow from the upper watershed into Calaveras and San Antonio reservoirs. Although controlled by San Francisco, the Commission provides water to cities and agencies that serve about 2.5 million people in San Francisco, San Mateo, Alameda and Santa Clara counties. In recent years, the SFPUC has vowed to be more environmentally friendly, and in 2006 it removed the Sunol and Niles dams on Alameda Creek. Although the dams were relatively low (about 10 and 15 feet, respectively) they were impassible by fish. The dams were also obsolete and had been since the SFPUC completed its Hetch Hetchy water project during the 1930s.

The SFPUC also joined 16 other public agencies in agreeing to collaborate on studies of stream flow and fish habitat needed for Alameda Creek steelhead restoration. While those studies are ongoing, several projects are planned or under way. Alameda County Water District and the Alameda County Flood Control District plan to build four fish passages, including a ladder at the BART weir. The water district also plans to remove a rubber dam; in May, the district installed fish screens at water diversion points. In addition, Pacific Gas & Electric has agreed to bury a pipeline that now acts as a barrier in the creek. Plus, agencies continue to convert old salt ponds into tidal marsh that are vital for salmon and steelhead fingerlings.

Once the creek projects are completed over the next three to four years, fish will be able to swim many miles upstream from the bay into potential spawning grounds. This winter, biologists rescued two fish (whom they named Bonnie and Clyde) that were stuck just below the BART weir and transported them upstream into Niles Canyon. Biologists believe Bonnie and Clyde successfully spawned the fry that were found swimming in Stonybrook Creek in late April.

But the big fight is coming over Calaveras dam. State inspectors in 2001 deemed the existing, 83-year-old earthen dam seismically unsafe and ordered the SFPUC to limit storage to 40% of capacity. The SFPUC intends to replace the dam with a new earthen structure just downstream of the existing dam. The project is part of a 20-year, $4.3 billion upgrade to the Hetch Hetchy system (see CP&DR Public Development, April 2002). A draft program EIR for the overall project found that the Calaveras dam replacement would have no impact on steelhead.

The Alameda Creek Alliance and other environmentalists rejected that conclusion. They contend the SFPUC should guarantee minimum flow rates in Alameda and Calaveras creeks to ensure a coldwater fishery can survive, and they want to see a fish ladder around the dam so that steelhead and possibly salmon could reach the upper portion of the watershed. They gained an ally in the National Marine Fisheries Service (NMFS), which in April told the SFPUC and the Army Corps to consult with NMFS on conserving fish and wildlife resources.

In a letter to the SFPUC, Richard Butler, supervisor of NMFS's Santa Rosa office, said that anadromous fish could reach the Calaveras dam site as soon as the construction stage. Thus, dam replacement "will affect steelhead by blocking access to historic headwater habitat and altering flow regimes in both Calaveras and Alameda creeks," Butler wrote.

Environmentalists also want a 32-foot-tall diversion dam, which directs water from Alameda Creek into Calaveras Reservoir, removed. Thus far, SFPUC has resisted that request. The dam reconstruction EIR remains under review.