San Joaquin Basin

Merced River

Environmental Data
Flow Temperature


The Merced River originates in Yosemite National Park and drains a 1,276-square-mile watershed in the southern portion of California’s Central Valley. Elevations range from 13,000 feet at its crest to 49 feet at the confluence with the San Joaquin River.

The Merced River has been affected by numerous human activities, including water storage and diversion, land use conservation, introduction of exotic plant and animal species, gold and aggregate mining, and bank protection.

During the 1950’s and 1960’s Merced River Chinook escapement averaged less than 500 fish in most years. Escapement began to increase substantially in 1970 following flow increases from the New Exchequer Dam and releases of hatchery-reared fish into the river. Since 1970, escapement in the Merced River has averaged approximately 5,300 fish with a peak of almost 30,000 Chinook in 1984.

Fisheries Monitoring

Juvenile Monitoring

Juvenile salmonid outmigration monitoring via rotary screw trap was conducted in the lower river at Hagaman County Park (RM 12.2) between 1998 and 2002 with funding from the Central Valley Project Improvement Act-Comprehensive Monitoring and Assessment Program (CVPIA/CAMP), and recently re-implemented in 2007 near Hatfield State Park (RM 2) with funding from U.S. Fish and Wildlife Service’s Anadromous Fish Restoration Program (USFWS AFRP). The objective of the lower river rotary screw trap monitoring is to document juvenile salmon outmigration and abundance.

Additionally, two side-by-side rotary screw traps were operated near Hopeton (RM 40) from 1999 through 2006 to assess Chinook salmon outmigration timing, abundance, and survival.

Adult Monitoring

Adult migration monitoring in the Merced River is conducted by two methods: (1) weekly carcass surveys and (2) enumerating Chinook by direct counts as they enter the Merced River Hatchery. Both methods target the fall-run Chinook migration period and are conducted by CDFG.

Carcass Surveys

The California Department of Fish and Game (CDFG) has been conducting escapement surveys in the Merced River since 1953. Data collected from the carcass surveys allow CDFG to estimate fall-run Chinook escapement; evaluate the distribution of redds in the study area; collect length and sex data; collect scale and otoliths for age determination and cohort analyses; and collect and analyze coded-wire tag data. Escapement estimates range from a high of 29,749 in 1984 to a low of 73 in 1990.

The escapement surveys cover a 24.7-mile reach extending from below the Crocker-Huffman Dam at the Merced River Hatchery (RM 51.9) to Santa Fe Road (27.1) and are divided into four sections: Merced River Hatchery to Snelling Road (RM 46.5); Snelling Road to Hwy 59 (RM 42.1); Hwy 59 to Shaffer Bridge (RM 32.5); and Shaffer Bridge to Santa Fe Road.

Two methods are used to estimate escapement each year, the Jolly-Seber and Schaefer mark-recapture methods. Using these mark-recapture methods, each carcass is tagged with a unique number by attaching an aluminum head tag to the lower jaw. Each tagged carcass is released back into the river near the lower end of the riffle then subsequently recovered during weekly surveys of the spawning areas. The weekly population estimates are obtained by calculating the ratio of recovered carcasses to the number of carcasses counted (i.e., counted fish include total fish tagged, skeletons and fresh carcasses that week).

Carcass surveys typically begin in October and continue through December to early-January depending on abundance and flow conditions.

Hatchery Counts

Chinook salmon enter a fish ladder and trap at the entrance of the Merced River Hatchery through an artificial spawning channel. Eggs and milt are harvested from salmon captured in the trap, then eggs are fertilized and incubated at the hatchery. Up to 1.1 million eggs are taken annually, resulting in a maximum of 960,000 smolts and 300,000 yearlings. Approximately 40 percent of the smolts produced at the hatchery are released back into the Merced River. Of the 40 percent that are released into the Merced River, 60 percent are released at the hatchery and the remaining 40 percent are trucked to different sites in the river. The remaining smolts not released in the Merced River are used for study releases on the Tuolumne, Stanislaus and San Joaquin rivers.