Statistical habitat models, such as generalized linear models (GLMs) and generalized additive models (GAMs), are key tools for assisting Ecosystem-based Fisheries Management (EBFM) efforts. These models can be used to map species distributions and assist in marine protected area (MPA) planning. In this study, the authors applied a statistical methodology to produce preference functions for fish and invertebrates along the West Florida Shelf, and then mapped the hotspots of juveniles and adults of three economically important species (Red Snapper, Gag, and Red Grouper) for informing future MPA planning. The analysis used a comprehensive survey database that included all encounter and nonencounter data of the study ecosystem collected by fisheries‐independent and fisheries‐dependent surveys. The REEF Volunteer Fish Survey Project dataset was one of 37 used in the analysis.