Pathfinder NWR consists of 16,807 acres and is an overlay project on part of the Bureau of Reclamation's Pathfinder Reservoir in south central Wyoming. The isolated refuge is located 50 miles southwest of Casper and 20 miles from the small settlement of Alcova, Wyoming.
The largest unit of this refuge lies astraddle of what is known as the Sweetwater Arm of the reservoir. The three smaller units are to the south of the Sweetwater Arm at Goose Bay, DeWeese Creek, and at the injunction of Sage Creek and the North Platte River. At low reservoir levels much of the refuge is bare mud flat with some marsh adjacent to the inlets. The upland portion is grassland interspersed with sagebrush flats. The upland portion of the refuge bounds the refuge in narrow strips, itself bounded by public lands used for grazing of livestock.