The lack of demographic data for many protected species often means that threats are poorly understood during recovery planning, and this results in difficulty defining sufficient metrics for assessing progress on recovery actions. The Neuse River Waterdog (Necturus lewisi) is a federally protected aquatic salamander endemic to the Neuse and Tar-Pamlico River basins of central and eastern North Carolina. It has quietly declined during four decades of intense urbanization, but the specific drivers of decline are unclear because there are no demographic data and only limited detection/non-detection information available. Our first objective was to clarify the drivers of decline by synthesizing the current knowledge of the hypothesized threats to N. lewisi. Because preexisting demographic data are lacking, we used prior natural history research and studies of ecologically similar species to develop hypotheses for the observed declines in occurrence. Our second objective was to update the knowledge of the species' current distribution throughout its historical range and then test our hypothesized threats using new occurrence data. We conducted detection/non-detection surveys across 116 locations throughout the species' historical range in two consecutive winter seasons (2018–2019 and 2019–2020) and modeled the effects of local and landscape variables representing three broad threat categories (pollution, flow suppression, and land use/land cover) using an occupancy modeling approach. We fit models representing all biologically relevant combinations of variables simultaneously, recognizing that threats are not independent in their effect. Dominant substrate type was the best predictor of occurrence and was negatively associated with the transition from cobble to silt (P < 0.05). Our analysis most supported the hypothesis that observed declines in the occurrence of N. lewisi are a delayed result of sedimentation-induced recruitment limitation. Uncertainty in the mechanism of decline remains because recruitment limitation could not be directly estimated with two years of occurrence data, yet this interpretation gained through an understanding of the species' underlying biology and current distribution contributes to the knowledge about present threats and will help guide and evaluate future recovery actions for this protected and narrowly endemic aquatic species.