According to the U.S. Census Bureau, the county has a total area of 588 square miles, of which 588 square miles is land and 0.1 square miles (0.02%) is water. Lyon County is the location of Gitchie Manitou State Preserve, which contains some of the oldest exposed bedrock in the country. Lake Pahoja is located in the northwest part of the county. It is a man-made lake with an area of just over 70 acres.