Nelson is located at the junction of the Mississippi River and Chippewa River valleys. The river bottoms surrounding the confluence are home to a large amount of wildlife. A causeway and bridge across the Mississippi River link Nelson with the city of Wabasha, Minnesota at the junction of Wisconsin Highway 25 and Wisconsin Highway 35. Southbound Highway 25 becomes Minnesota Highway 60 upon crossing the Mississippi River to Wabasha.
Nelson lies on Wisconsin Highway 35, the "Great River Road," a popular tourist route that runs along the east bank of the Mississippi River. The village's primary destination for tourists is the 100-year-old Nelson Cheese Factory.