Williams County lies on the west edge of North Dakota. Its west boundary line abuts the east boundary line of the state of Montana. The Missouri River flows eastward along the county's south boundary line. Horse Creek and Willow Creek flow to the west across the upper portion of the county. The terrain consists of isolated hills amid rolling hilly semi-arid stretches. The area is partly devoted to agriculture. The terrain is highest across its midpoint, and slopes to the NW and SE. Its highest point is a hill near the NE corner, at 2,470' (753m) ASL. The county has a total area of , of which is land and (3.3%) is water. It is the fourth-largest county in North Dakota by area.