Merced River Hatchery

The last three miles to the Merced River Hatchery run along the gravel bank of an irrigation canal. From Merced the route goes north on Highway 59, right onto Snelling Road, left onto Robinson Road, and left again onto the canal bank just before the road crosses it. From there the visitor follows signs. The California Department of Fish and Wildlife calls the place “a little tricky to find.”

At the end of the road the Merced River comes out below Crocker-Huffman Dam, the point past which salmon cannot climb. The hatchery sits immediately downstream, about 15 miles northeast of Merced in Merced County. It is open to the public from 8:00 a.m. to 3:00 p.m. and has views of the river and the wildlife that uses it, along with public restrooms. The fish ladder usually opens to spawning fish on October 1.

Fall Chinook at the ladder

The hatchery spawns, rears and releases fall-run Chinook salmon of Merced River origin. A 2012 statewide hatchery review, reprinted by the department, lists fall Chinook as the only species reared here. The review calls the program experimental: its releases test how the survival of young fish to adulthood varies from one release site to another.

The production goal is to take two million eggs and release one million smolts, each about 80 millimeters in fork length, between late April and mid-May. Some fish are released at the hatchery and others at points on the lower Merced, on the San Joaquin River, and farther downstream. A constant quarter of them have the adipose fin clipped and carry a coded wire tag.

Returning adults enter through the ladder of the old spawning channel. A 1989–90 annual report describes the trap built into it: a fyke entrance, two basket hoists, an anaesthetic tank, a sorting table, and holding pens. That season the trap opened October 23 and the first salmon arrived November 5. The count ended at 82 fish. The same report records 927 visitors, with tours given to organized groups and schools.

A loop of gravel, 1970

Salmon “had all but vanished from the river during the mid-1960’s,” Robert S. Menchen of the Department of Fish and Game wrote in 1971. The main cause was low fall flows. In some years there was too little water even for spawners to ascend the river, and spawning gravel was scarce as well.

The Merced Irrigation District built the remedy with part of the Davis-Grunsky Act funds it received from the Department of Water Resources for recreation and fish enhancement. Under that grant the district guaranteed 180 to 220 cubic feet per second in the river from November to April. The department’s later history adds a second purpose: mitigation for habitat lost to the Crocker-Huffman, Merced Falls and Exchequer dams. The district’s own website points to an older alteration of the river. Gold dredging from the mid-1800s into the mid-1900s stripped the streambed and left the rock piled in rows along the banks.

The project was a spawning channel 4,372 feet long, laid out as one loop of spawning sections and resting pools, and later named the Reuben E. Schmidt Spawning Channel. Water entered from the reservoir behind the dam through a diffusion chamber and welled up evenly, which discouraged fish from jumping and hurting themselves. Salmon came in from the river by a three-step fishway. The channel was designed for 12,000 spawners. Menchen reported it completed in the summer of 1970, and water was first let in on October 20, 1970. Salmon began entering as soon as it filled.

The first season went partly wrong. In early November, water pressure forced out a section of the grill over the diffuser. About 100 salmon passed into the reservoir above the dam, and fishermen caught many of them. Carcass counts did not begin until November 21. After that, crews walked the riffles and drifted the resting pools in a small boat to recover the dead from the bottom.

By mid-April the river was too low for young salmon to reach the sea, and Menchen decided to truck them to the Delta. Fish were held a week at a time in a live box and driven to a release point near the Antioch Bridge. After the second week, in his words, “it was evident outmigrant trapping and trucking was not a paying proposition.” On May 10, crews seined an estimated 30,000 fingerlings from the channel, working through thick mats of algae, and hauled them in a 600-gallon tank truck to the bridge. Menchen put the season’s survival from egg to outmigrant at 38.7 percent.

The dam’s own fish ladder was closed in the 1970s to test whether the channel beside it would serve salmon, steelhead and other fish better. A Fish and Game letter of March 25, 1971, quoted in a later legal opinion, records the request that the district make the dam ladder inoperable so salmon would turn into the channel.

Ponds, silver salmon, and a counting trap

A gravel rearing pond went into use on April 26, 1971, when more than 100,000 Stanislaus River fingerlings arrived from Moccasin Creek Hatchery. In October, 86,000 of them went into the Merced as yearlings. A second pond followed in February 1972. That August a fish culturist was assigned to live at the site; before then, district employees and seasonal Fish and Game aides had run the place.

In the spring of 1972, algae plugged the downstream-migrant screen faster than it could be cleaned. District crews fixed the problem by burying pipes under a gravel dam built across the channel. “The perforated pipes passed the water, the open pipes passed the fish, and the dam held the algae back,” Menchen wrote.

Chester O. Chase reported that use and production in 1973–74 were the highest in the facility’s history. On December 1, 1973, the department and the district agreed on a third pond for silver salmon. The state would keep the first 100,000 fish for an experiment: planting yearlings in Southern California estuaries in an attempt to establish an offshore salmon fishery. The next 10,000 would go to McClure Reservoir for the district. The pond was built in January 1974 and stocked in March with 226,800 fry. Shortly afterward, many of them apparently burrowed through the gravel into the water supply pipe and came out in the spawning channel and the first pond.

Through 1978–79, each run’s size was estimated from redds and carcasses. Beginning in fiscal 1979–80, a trap ran through every spawning season and the fish were counted. The tables in the annual reports run from 99 salmon in 1970–71 up to 1,795 in 1983–84, then back down to 82 in 1989–90.

In the drought of 1989, returning fish were drawn up the San Joaquin by irrigation drain water. The department trapped them at a weir beside the Los Banos Wildlife Area, with electrical cables strung across Salt and Mud sloughs to turn them, and carried the eggs to Merced. That same year the facility supplied eyed eggs to four Merced County elementary schools, the first classroom-incubator projects in the San Joaquin Valley. Dr. Ron Hedrick of the University of California, Davis, also tested the drug Fumagillin DCH there against proliferative kidney disease. On May 11, 1990, more than 118,000 young salmon were moved to the Tuolumne River to clear the way for new raceways and a water line.

Kidney disease, cold water, and a failed experiment

During the 1980s and 1990s the facility was converted into a spawning and rearing hatchery to increase production. The sources date its beginnings differently. The irrigation district’s website says the district built the hatchery with the state wildlife department in the late 1970s. A 2000 assessment of Central Valley Chinook salmon dates the start of operation to 1971.

The yearling program ended after heavy losses to proliferative kidney disease, which is caused by Tetracapsuloides bryosalmonae, a parasite native to the Merced. In a November 2009 letter, quoted in the same legal opinion, the department said the spawning-channel experiment had failed and that additional management actions were needed for the river’s anadromous fish.

In September 2015, Delta Hydronics and Integrated Aqua Systems supplied a chilling system that uses the cold water leaving the hatchery to pre-chill the river water coming in. During a later drought, emergency funds made available by Governor Brown and the legislature bought temperature-controlled tanks. Sixty rainbow trout rescued from the river lived in them for 18 months. Spawned at the hatchery, they produced hundreds of offspring, and the department returned the fish to the Merced.

A February 2025 engineering study examined 21 department hatcheries for vulnerability to climate change. At Merced it found an intake that clogs with debris and an ultraviolet disinfection system unable to treat the 3 cubic feet per second that runs through the raceways. It also found an incubation building too small to finish early rearing indoors, so undersized fry are moved early to covered outdoor tanks. The alternative the study selected replaces the raceways with circular tanks.