There is increasing concern over how Arctic fauna will adapt to climate related changes in sea-ice. We used long-term sighting and genetic data on beluga whales (Delphinapterus leucas) in conjunction with multi-decadal patterns of sea-ice in the Pacific Arctic to investigate the influence of sea-ice on spring migration and summer residency patterns. Substantial variations in sea-ice conditions were detected across seasons, years and sub-regions, revealing ice–ocean dynamics more complex than Arctic-wide trends suggest.