Anthropogenic influences like land use and climate variability interact with natural heterogeneity to influence the persistence of stream salamanders. Using occupancy modeling in the southern Appalachian Mountains, we investigated the influence of land use, climate, and physical context (e.g., drainage area, elevation) on stream salamander occupancy, noting species, and life stage specific responses. Our results illustrate that forest loss is a better predictor of salamander occupancy than physical context (elevation) or climate. Across the gradients in this dataset, precipitation did not have a significant influence on salamander occupancy, potentially due to the observed narrow, wet gradient. Temperature had little effect on Eurycea wilderae occupancy; however, temperature negatively affected adult but not larval Desmognathus amphileucus occupancy. Spatial thermal variability in this study was larger than projected increases due to climate change, suggesting that local mechanisms (e.g., behavior or physiological plasticity) may facilitate salamander resilience to climate change. However, the negative effects of forest loss coupled with rising temperatures (e.g., increased solar radiation, warmer stream runoff) underscore the importance of riparian forests in mitigating climate stressors. Preserving forest cover is critical for maintaining stream salamander populations and may offer opportunities for maintaining resilience in the face of additional stressors like rising temperatures or drought.