With the rise of environmental niche modeling, it has become popular to project how climate change will alter the distribution of a species. Such models extrapolate future dynamics based on contemporary correlations between species occurrence and climate. When lacking a mechanistic basis, these models are useful mainly to prompt further research. For example, the American pika (Ochotona princeps) has been predicted to lose a majority of currently suitable habitat during this century under some climate projections, but these projections are not linked mechanistically to the microclimates used by these sub-surface specialists. We have investigated a mechanistic basis for pika population dynamics by relating individual survival and physiological stress to the microclimates that pikas experience. During 2008-2013, pikas were marked, sampled and released at Niwot Ridge and several other study sites in the south-central Rocky Mountains, USA. Blood and fresh fecal samples were collected for enzyme-immunoassay analyses to measure acute and chronic stress in each pika, indexed by glucocorticoid stress hormones and their metabolites. Survival of marked pikas was estimated via program MARK using an annual re-sight protocol. Microclimatic data were collected using temperature data loggers positioned in each marked pika’s territory. Individual survival was well predicted by our metric of chronic stress: pikas that survived one year after sampling (N = 33) had initial stress hormone levels almost 60% lower than pikas that did not survive (N = 49). We further characterized relationships between microclimate, stress metrics and individual survival using structural equation models. Results suggest mechanistic effects of microclimate on physiological stress and survival. In order to project pika dynamics into the future, it will be necessary to characterize how changes in macroclimate affect changes in the sub-surface microclimates of blocky debris--the microhabitat used by pikas. We present our methods as a feasible approach for characterizing mechanistic relationships that drive population and range dynamics.