La Crosse's source of water is an aquifer consisting of a deposit of glacial outwash sand and gravel in the valley of the pre-glacial Mississippi River. This sand and gravel aquifer is approximately 170 feet in depth in the La Crosse area and is bounded on the east by the bluffs and on the west by the Mississippi River.

It is the responsibility of the Water Utility department to operate and maintain all the grounds, buildings and equipment of the city to include 15 wells, 1 reservoir, 220 miles of water main and the main pumping station.