Accurate assessment of species distribution is a critical component in conservation planning. We utilized a multi-method approach to assessing the distribution of Cryptobranchus alleganiensis (Hellbender) and the habitat the species occupies in the New York portion of the Susquehanna River watershed, including a ground-validated species-distribution model (SDM), visual assessment of rock cover, rock-lifting surveys, and eDNA sampling. Suitable rock cover was sparsely distributed, and Hellbender distribution was limited to a small subset of the study area. Hellbenders were detected at 9 of 22 historic sites, suggesting considerable decline. Only a single individual was captured, but eDNA identified Hellbender presence at 13 of 51 sites. We suggest that a multi-method approach integrating SDM and eDNA is more effective for monitoring low-density populations than traditional field methods alone.