Three Sisters Springs was a forested wetland to be developed with condos and the spring water was intended to be commercially extracted. In order to protect manatee, improve access to the springs and restore native habitat the land was purchased in 2010 with funds from the Florida Community Trust, the City of Crystal River, U.S. Fish & Wildlife Service (USFWS), Southwest Florida Water Management District (SWFWMD), many community members and non-profit groups. The City and SWFWMD jointly own the land, and it is managed by USFWS under the Crystal River National Wildlife Refuge Complex (CRNWR).

In 2011, construction began to encircle the springs area with a 1,600-ft boardwalk for visitors to view the wintering manatees.