According to the U.S. Census Bureau, Waterloo has a total area of , of which are land and , or 1.61%, are water. The city sits on a ridge that drains east to tributaries of Prairie du Long Creek and west to tributaries of Fountain Creek. Prairie du Long Creek is a southeast-flowing tributary of the Kaskaskia River, while Fountain Creek is a west-flowing direct tributary of the Mississippi River. Waterloo is along the historic trail that went from Kaskaskia to St. Louis.
according to the us census bureau waterloo has a total area of  of which are land and  or 161% are water the city sits on a ridge that drains east to tributaries of prairie du long creek and west to tributaries of fountain creek prairie du long creek is a southeast-flowing tributary of the kaskaskia river while fountain creek is a west-flowing direct tributary of the mississippi river waterloo is along the historic trail that went from kaskaskia to st louis