Gulf Sturgeon (Acipenser oxyrinchus desotoi) are a threatened anadromous fish species which are reliant on rocky substrates in freshwater river systems for spawning. Several spawning grounds have been documented across the Suwannee, Apalachicola, Choctawhatchee, Yellow, and Escambia river basins which comprise the eastern extent of the species range. In contrast, only one spawning ground has been located on the Pascagoula river basin while no spawning grounds have been identified on the Pearl river basin. Effective restoration of the Pearl and Pascagoula Gulf Sturgeon populations requires information on the extent and location of potential spawning grounds to evaluate the quality and prioritize restoration of these habitats. Recreation-grade side scan sonar (SSS) instruments, or fishfinders, have proven an effective tool for rapidly surveying river habitats. However, existing methods for processing sonar mosaics and generating substrate maps requires a high degree of human-intervention and expertise, which limits the accessibility, efficiency, and reproducibility of these approaches. To address this issue, we developed a new open-source and freely available Python-based software called PING-Mapper to map suitable spawning substrates in these systems. PING-Mapper is an end-to-end framework for surveying and mapping aquatic systems at large spatial extents reproducibly, with minimal intervention from the user. Over 1,000 km of river habitats have been imaged with Humminbird® side imaging systems and PING-Mapper workflows have automatically predicted and mapped substrates with deep neural network models trained on data from the Pearl and the Pascagoula. The new maps provide a means of identifying reaches with potential Gulf Sturgeon spawning grounds across this large spatial extent, which will contribute to the recovery of the species.