Eastern Hellbender (Cryptobranchus alleganiensis alleganiensis) populations are experiencing drastic declines range-wide. Effective conservation strategies require understanding the environmental factors underlying population occurrence within the stream networks that Eastern Hellbenders inhabit. We contrasted habitat elements between historically occupied and apparently unoccupied sites throughout the Susquehanna River Basin in New York, an area that represents the northernmost segment of the species' range. Historically occupied sites contained larger rocks and less soft sediment than unoccupied sites. Regional-scale predictive models of Eastern Hellbender distribution in Pennsylvania indicated that specific geologic features—loamy till, clayey to loamy till, and mixed origin sand and gravel deposits—as well as extensive forest cover were the strongest predictors of Eastern Hellbender occurrence. We conclude that occurrence is dependent on isolated and uncommon geological features that cause the species' distribution to be highly patchy and that stream sedimentation is a major threat to this species in its northern range. Our research also indicates that predictive modeling can be useful in examining drivers of Eastern Hellbender distribution and targeting regions for population surveys and habitat conservation.