The Freshwater Institute, located in Shepherdstown, is a program of the Conservation Fund, a nonprofit organization whose mission is to create partnerships among industry, nonprofit organizations, and government agencies to advance land and water conservation in the United States. The fund has also developed activities focused on demonstrating the sustainable use of natural resources, including the Freshwater Institute.

The Freshwater Institute was launched in 1987 and is a national program, although the 13-state Appalachian region is the core operating area. It works to improve and protect water quality and conserve watersheds while promoting rural growth and development. The work of the institute has focused on aquaculture or fish farming research and development; rural economic development; entrepreneurial training and education; acid mine drainage remediation; and community assistance. The institute's facilities include research laboratories, classroom-workshop space, fish culture systems, greenhouses, constructed wetlands, and other conservation demonstration projects. Some specific projects include an inventory and development of new, cost-effective treatments for acid mine drainage that will help waters return to their healthy states; development of an aquaculture education curriculum and teacher training workshops; and the first integrated aquaculture-hydroponic system powered by free natural gas.

As of 2023, the institute had saved 113,159 acres of land and water, protected more than 14,700 acres in partnership with U.S. Fish and Wildlife, and protected more than 51,900 acres of forest lands in West Virginia.