The Rapid River watershed is the third smallest watershed on the Minnesota side of the Rainy Lake Basin. Like its neighbors, the Rapid River watershed is characterized by extensive wetlands located on the Glacial Lake Agassiz lake bed. This once-glaciated area is part of the Agassiz Lowlands region. Soils are generally sandy loams, with considerable deposits of glacial till and outwash over a bedrock residuum. Elevation in the watershed ranges from 1,060 to 1,310 feet above sea level, with the highest values being in the western and northwestern portions of the watershed. Lower elevations are found across the northeastern regions near where the Rapid and Rainy Rivers meet.
As with many areas of northern Minnesota, principal industries include forest product harvesting, forest product manufacturing, farming, and tourism. Much of the land in the watershed is not suited or is poorly suited to agricultural uses. Wetlands (74.8%) make up most of the watershed, Agricultural accounts for only 3% of the total acres. Development pressure is moderate throughout this watershed, with occasional lands being parceled out for timber production or recreational use.
The main resource concerns in the watershed are soil erosion, management of excessive wetness, wetland and woodland management, pasture management and surface water quality.