Browns Valley lies along the Little Minnesota River between the northern end of Big Stone Lake and the southern end of Lake Traverse, which is separated from the Little Minnesota River by a low and narrow continental divide that skirts the northern edge of town. The city, both lakes, and the river lie in the Traverse Gap, the bed of ancient, south-flowing Glacial River Warren, the outlet to Glacial Lake Agassiz which, when drained, became the valley of the north-flowing Red River of the North.