Winter flounder (Pseudopleuronectes americanus) have declined to less than 11% of their historical abundance in offshore areas and have experienced severe declines and inbreeding in coastal subpopulations. Understanding metapopulation structure and disparate migratory behavior is vital to understanding the species’ dynamics. We used acoustic telemetry to evaluate migratory types, homing behavior, and spawning behavior in adult winter flounder (n = 72) in Mattituck Creek, New York. Telemetry results showed that 17% of the tagged individuals displayed resident behavior and remained in the creek year-round despite mean summer temperatures reaching 28 °C. Alternatively, the migratory group (∼83%) started to leave the system when the mean water temperature reached 12 °C. A dominant driver of migration was not indicated; instead, migration out of or into the creek appeared complex and related to date, temperature, lunar cycle, photoperiod, and year. Approximate spawning was estimated to occur as early as November and continued through April based on aggregative behaviors of adults and back-calculations of dates using young-of-the-year otoliths. Our results support the emerging view that winter flounder’s dynamics reflect local life history and population diversity, which are currently unaccounted for in management.