Recreational motor boating in shallow water can damage submerged natural resources through propeller scarring and these impacts represent one of many factors that affect the health of seagrass ecosystems. Understanding the patterns of seagrass scarring and associations with physical and visitor-use factors can assist in development of management plans that seek to minimise resource damage within marine protected areas. A quantification of seagrass scarring of Florida Bay in Everglades National Park, using aerial imagery, resulted in the detection of a substantial number and length of seagrass scars. Geospatial analyses indicated that scarring was widespread, with the densest areas found in shallow depths, near navigational channels, and around areas most heavily used by boats. Modelling identified areas of high scarring probability, including areas that may experience increased scarring in the future as a result of a reallocation of impacts if management strategies are implemented. New boating-management strategies are warranted to protect seagrass in Florida Bay. An adaptive approach focusing on the most heavily scarred areas, should consider a variety of management options, including education, improved signage, new enforcement efforts and boating restrictions, such as non-motorised zones, or temporary closures. These methods and recommendations are broadly applicable to management of shallow water systems before and after resource impacts have occurred.