National Mitigation Fisheries Coordination Act - Directs the U.S. Fish and Wildlife Service (USFWS) to impose a charge for conducting mitigation fishery activities in connection with federal water resources development projects carried out by water development agencies (Army Corps of Engineers, the Bureau of Reclamation, or the Tennessee Valley Authority [TVA]). Requires such agencies to pay the charge in accordance with a fishery mitigation plan developed and approved by the USFWS Director and the agency head.

Defines "mitigation fishery activities" as rearing and stocking of native and nonnative fish to replace or maintain fishery resources or harvest levels lost as a result of such a project, including project planning, population assessment and evaluation, genetic monitoring, broodstock development, and fish health sampling.

Requires USFWS's charges to be reasonably related to expenditures necessary to: (1) operate, maintain, and rehabilitate certain USFWS-owned and -operated mitigation fishery facilities, hatcheries, and health centers; and (2) conduct mitigation fishery activities, including expenditures for personnel, transportation, utilities, contractual services, fish feed, supplies, equipment, routine maintenance, deferred maintenance, fish eggs, technical support, fish health, management and administration, planning, outreach and education, and hatchery product evaluations.

Sets forth a listing of applicable mitigation fishery facilities in Arkansas, Georgia, Kentucky, Missouri, Montana, North Dakota, Pennsylvania, South Dakota, Tennessee, Utah, West Virginia, Wisconsin, and Wyoming.