The West Virginia Division of Natural Resources operates seven coldwater fish hatcheries and two warmwater fish hatcheries.

The coldwater fish hatcheries produce catchable-sized trout for the state's statewide stocking program. Rainbow, golden rainbow, brook, and brown trout are raised. The hatcheries are located primarily in the mountains of east-central West Virginia to take advantage of the many springs in that region of the state. The hatcheries hatch, raise, and stock fish.

Petersburg Hatchery, built in the early 1930s, is located near Petersburg in Grant County. It produces catchable-sized fish and provides rainbow and golden rainbow eggs and fingerlings to other hatcheries. Ridge Hatchery, located in Morgan County near Berkeley Springs, was also built in the early 1930s. It stocks trout in many of the streams and small impoundments in the Eastern Panhandle. Edray Hatchery, near Marlinton in Pocahontas County, was built in the 1930s and expanded in the 1940s.

Spring Run Hatchery is located near Dorcas in Grant County. This hatchery was constructed in the early 1950s at one of West Virginia's largest springs, which supplies about 3,000 gallons per minute. Spring Run is one of the largest hatcheries operated by the Division of Natural Resources, and supplies trout for stocking by the smaller hatcheries. Bowden Hatchery, another large hatchery, is located near Elkins in Randolph County. It was constructed by the U.S. Fish and Wildlife Service in the early 1960s and transferred to the state in 1997. Bowden's annual trout production was similar to Spring Run but has been expanded by 50 percent in recent years.

Reeds Creek Hatchery, located west of Ruddle in Pendleton County, was completed in 1979. Unique among West Virginia's trout hatcheries, Reeds Creek filters and re-uses 80 percent of its water. Reeds Creek, like Spring Run, provides trout to the smaller hatcheries that have low summer flows, and also transfers catchable-sized trout in the spring for stocking by other hatcheries.

Tate Lohr Hatchery is located near Oakvale in Mercer County and was also completed in 1979. It stocks much of southern West Virginia. This hatchery is a small rearing facility, and the majority of its trout are hauled in by Reeds Creek and Spring Run hatcheries during the spring.

The seven coldwater hatcheries annually produce and stock approximately 750,000 pounds of trout in 200 streams and small impoundments scattered across the Mountain State. Between January and May 2023, the DNR stocked 802,481 trout, a 19 percent increase from the previous year.

Palestine Warmwater Hatchery near Elizabeth, Wirt County, has been in operation since the 1930s. Apple Grove Warmwater Hatchery near Apple Grove, Mason County, opened in 2001. Walleye, musky, channel catfish, blue catfish, hybrid striped bass, largemouth bass, smallmouth bass, and striped bass are raised at the warmwater hatcheries and stocked into streams and lakes across the state.

West Virginia is also home to a federal fish hatchery operated by the U.S. Fish and Wildlife Service. The White Sulphur Springs National Fish Hatchery raises rainbow trout eggs that are shipped to 20 fish hatcheries across the country. After the eggs are shipped, the trout are then provided to the West Virginia Division of Natural Resources, the Maryland Department of Natural Resources, and the Eastern Band of Cherokee Nation. Since 1995, the federal hatchery has also raised freshwater mussels to improve wild populations of the endangered creatures. It also raises endangered crayfish and candy darters.