Conservation of species facing environmental change requires an understanding of interpopulation physiological variation. However, physiological data is often scarce and therefore pooled across populations and species, erasing potentially important variability between populations. Interpopulation variation in thermal physiology has been observed within the Salmonidae family, although it has not been associated with seasonally distinct migratory phenotypes (i.e., seasonal runs). To resolve whether thermal physiology is associated with life-history strategy we acclimated four Sacramento River juvenile Chinook salmon populations (Coleman fall-run, Feather River fall- and spring-run and Sacramento River Winter-run) exhibiting different seasonal migratory phenotypes (fall-, spring- and winter-run), at 11, 16 and 20°C and assessed variation in growth rate, critical thermal maxima and temperature-dependent metabolic traits. We identified population differences in the physiological parameters measured and found compelling evidence that the critically endangered and endemic Sacramento River winter-run Chinook population exhibits thermal physiology associated with its early-migration life-history strategy. Acclimation to warm temperatures limited the growth and metabolic capacity of winter-run Chinook salmon, highlighting the risk of future environmental warming to this endemic population.