Amphibians are currently facing widespread population declines, primarily due to the introduction of anthropogenic stressors, which have the potential to alter ecosystem dynamics and elicit long-term physiological responses resulting in overall population declines. Population assessments typically rely upon genomics, demography, and geographic isolation; however, when physiological parameters are included, mechanistic explanations for population declines can be determined. Rapid population assessments that can be related to specific microhabitat characteristics for management purposes can be achieved by implementing a chronic stress proxy, such as neutrophil: lymphocyte (N:L) ratios. As a long-lived habitat specialist, facing dramatic population declines with state and federally protected populations, the Hellbender (Cryptobranchus alleganiensis) is a good candidate species for applying N:L ratios to assess population vulnerability and habitat quality. This study used N:L ratios as a proxy of chronic stress among Hellbender populations to determine environmental variables potentially correlated with chronic stress. Additionally, comparisons of N:L ratios were made among Hellbender populations to examine applicability of this method for assessing amongpopulation differences. Of the microhabitat variables assessed, high conductivity, low pH, and low dissolved oxygen correlated with elevated N:L ratios. In addition, N:L ratios differed significantly among Hellbender populations, which suggests the utility of N:L ratios as an indicator of population-level differences. Specifically, where traditional methods lack the ability to detect concerns, physiological assessment suggested certain populations may be of concern in regard to experiencing chronic stress. Including physiological parameters in viability and vulnerability assessments more frequently, such as the one described here, can provide evidence of population concerns earlier than traditional methods, and allow for better management strategy by elucidating specific environmental variables contributing to stress.