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Freshwater ecosystems are impacted by anthropogenic stressors, resulting in roughly one-third of freshwater fauna being threatened with extinction. The Neuse River Waterdog (<i>Necturus lewisi</i>) is a large aquatic salamander endemic to the Neuse and Tar-Pamlico River basins of eastern North Carolina, USA, and it was listed as threatened under the federal Endangered Species Act in 2021. Habitat degradation has been identified as the dominant threat driving <i>N. lewisi</i> occurrence, and its effect may be delayed. The USFWS Draft Recovery Plan classified investigation into the species' occurrence dynamics (colonization/extinction) as a high priority action. We hypothesized that extinction probabilities would decrease in high quality local instream habitats, increase with high proportions of disturbed land cover in the contributing watershed, and increase in years with intense droughts. We evaluated these hypotheses within a dynamic occupancy modeling framework using five consecutive years of detection/non-detection data collected across 176 locations. We derived estimates of annual occurrence, turnover, and equilibrium occupancy (stability) to investigate if spatial responses to threats were delayed-an extinction debt. The top-ranked model supported the hypotheses on drivers of site-specific extinction probabilities, including a negative effect of habitat quality, positive effect of developed land cover in the watershed, and positive effect of annual drought intensity. The derived estimates broadly indicated that annual occurrence was highest in rural subpopulations (i.e., management units), turnover was greatest in urban subpopulations, and equilibrium occupancy was lower than required to maintain stability in most subpopulations of the Neuse River basin. The estimated occurrence dynamics and their derived quantities suggested an extinction debt in urban subpopulations that may be accelerated by stochastic drought events. This study describes a novel use of the dynamic occupancy model framework within an extinction debt context and provides partnering conservation agencies with information important to guiding recovery of the Neuse River Waterdog.