Rainbow Springs Aquatic Preserve is located in southwest Marion County. The aquatic preserve includes the length of the Rainbow River and was designated in 1986 for the purpose of maintaining the springhead and river run in essentially natural condition. Rainbow Springs State Park surrounds the headsprings and follows much of the east bank of the river.

The Rainbow Springs run is one of the largest spring runs in the world. It averages a discharge of over 400 million gallons of water per day. The run is 5.7 miles long and joins the Withlacoochee River which is a black water river, near the town of Dunnellon. It is characterized by a high level of submersed aquatic plants. Ribbon or tape like plants are the most common.

Its waters have an average temperature of 72 degrees Fahrenheit year round. Because of this and the high water quality, it is a very popular recreational destination.