The Kings Bay, Crystal River complex, located in Citrus County, Florida, is one of the world's largest spring-fed ecosystems and a critical warm-water refuge for endangered Florida manatees. Unfortunately, large areas of Kings Bay are currently in a state of ecological degradation characterized by smothering mats of the filamentous cyanobacterium Lyngbya wollei. The causes of this ecosystem shift are not well understood, although it is often suggested that human-caused nutrient loading into the Bay combined with intermittent saltwater intrusions from storm surges may be responsible. In this article, we present results from interviews with local citizens, a review of aquatic plant literature, and research into the history of ecological change in Kings Bay. Our work indicates that management efforts to eradicate invasive exotic aquatic species may also have played an important role in the dominance of L. wollei. We suggest that future restoration efforts should follow a logic of "alternative stable states" that focuses primarily on the recovery of desired ecosystem functions and relaxes the assumption that exotic plants should be minimized. The Kings Bay case study points toward a more adaptive conception of ecological restoration, one informed by local knowledge and open to the utilization of established exotic plants as a tool for maintaining or restoring important ecological attributes.