The La Crosse-Bad Axe River Basin encompasses approximately 1,000 square miles in southwest Wisconsin. This basin lies entirely within the portion of Wisconsin that was not flattened by the glacial ice drifts, also known as the driftless area. The basin is divided into six watersheds for water resource management purposes: Upper La Crosse River, Little La Crosse River, Lower La Crosse River, Coon Creek, Bad Axe River, and the Rush Creek watersheds.
Three watersheds drain to the La Crosse River,
while the other three drain directly toward the Mississippi River.