The Cheyenne River flows east-northeastward along the southern boundary of Ziebach County. The Moreau River flows eastward through the upper portion of the county, and Cherry Creek flows southeastward through the lower portion, draining the area into the Cheyenne River. The terrain is composed of semi-arid rolling hills interrupted by buttes and carved by drainages and gullies, partly devoted to agriculture and cattle. The terrain slopes to the south and the east; its highest point (except for the isolated Thunder Butte, at 2,733') is near its NW corner at 2,582' (787m) ASL. The county has a total area of , of which is land and (0.5%) is water. Almost the entire county lies within the Cheyenne River Indian Reservation. The balance of the county, along its extreme northern county line, lies within the Standing Rock Indian Reservation. It is one of five South Dakota counties that lie entirely on Indian reservations.