Animals confront thermoregulatory constraints that define species ranges, impact productivity, and limit their ability to cope with long-term environmental change. Marine poikilothermic species are assumed to have a body temperature comparable to ambient temperatures as well as possess a limited ability to behaviorally regulate body temperature. Winter flounder Pseudopleuronectes americanus is a migratory species with a complex life history that places it in environments that exceed the species' thermal tolerance. To determine if winter flounder use temperature refuge during seasonally cold and warm periods, we evaluated internal body temperature relative to water temperature, utilizing acoustic telemetry in a southern New England estuary. The internal body temperature of individuals commonly exceeded that of ambient water during the winter, and conversely, remained lower than ambient water during the summer. During a 3 mo trial, Kalman filter time series analysis indicated that internal body temperatures of winter flounder exhibited greater similarity to sediment temperature recorded at depths of 3, 6 and 9 cm compared to water temperature, indicating that winter flounder use burial as a strategy for thermoregulation. Such discoveries have the potential to transform our understanding of the complex interaction between environmental conditions and behavior, providing critical insight into phenomena that underpin species' life history strategies.