Brook trout (Salvelinus fontinalis) are common in waters ranging from the Appalachian Mountains to the Arctic Circle. These popular, coldwater sport fish face an uncertain fate in light of several climate change scenarios. Assessing the potential influence of variable temperature on brook trout populations poses an important challenge to fisheries biologists. I conducted a robust design mark-recapture study in three lakes in New York's Adirondack Park to estimate population parameters related to survival, abundance, detection probability and movement under contrasting thermal conditions. Results from candidate model set comparisons support the hypotheses that brook trout living in unstratified lakes experienced reduced survivorship in hot, dry years, while fish living in nearby, stratified lakes did not. Furthermore, chronic thermal stress metrics, when added as covariates, received significantly more support in the model set than acute metrics, (i.e., maximum water temperature), highlighting the relative importance of cumulative thermal stress on adult survival.