Freshwater mussels (Unionidae) are among the most imperiled groups of organisms in the world, and the lack of information regarding species distributions, life-history characteristics, and ecological and biological requirements may limit the protection of remaining mussel populations. We examined the influence of hydrologic factors on the occurrence of the Suwannee Moccasinshell Medionidus walkeri, a federally threatened freshwater mussel species, endemic to the Suwannee River Basin in Georgia and Florida. We also evaluated the influence of survey effort on detection of Suwannee Moccasinshell during field surveys. We compiled all recent (2013–2016) mussel survey records in the Suwannee River Basin. We calculated cumulative discharge contributed by upstream springs for each of 220 survey locations. We combined the spring discharge predictor variable with Suwannee Moccasinshell detection and nondetection data from each survey location to develop a suite of occupancy models. Modeling results indicated that detection of Suwannee Moccasinshell during surveys was strongly and positively related to survey effort. Modeling results also indicated that sites with cumulative spring discharge inputs exceeding ∼28 cubic meters per second were most likely (i.e., predicted occupancy probabilities >0.5) to support Suwannee Moccasinshell populations. However, occupancy declined in the lowermost reaches of the Suwannee mainstem despite high spring discharge inputs, presumably due to greater tidal influences and differences in physicochemical habitat conditions. Historical localities where Suwannee Moccasinshell has presumably been extirpated are all devoid of springs in their upstream watersheds. We hypothesize that springs may buffer extremely tannic, and at times polluted, surface waters, in addition to maintaining adequate flows during periods of drought, thereby promoting the persistence of Suwannee Moccasinshell populations. Our study suggests that springs are a critical resource for Suwannee Moccasinshell and may be more important for conservation planning than was previously recognized.