According to the U.S. Census Bureau, Junction City has a total area of , of which , or 2.56%, are water. The village drains south to tributaries of Crooked Creek, a west-flowing tributary of the Kaskaskia River.
according to the us census bureau junction city has a total area of  of which  or 256% are water the village drains south to tributaries of crooked creek a west-flowing tributary of the kaskaskia river