The Northwest Atlantic marine ecosystem off Newfoundland and Labrador, Canada, has been commercially exploited for centuries. Although periodic declines in various important commercial fish stocks have been observed in this ecosystem, the most drastic changes took place in the early 1990s when the ecosystem structure changed abruptly and has not returned to its previous configuration. In the Northwest Atlantic, food web dynamics are determined largely by capelin (Mallotus villosus), the focal forage species which links primary and secondary producers with the higher trophic levels. Notwithstanding the importance of capelin, the factors that influence its population dynamics have remained elusive. We found that a regime shift and ocean climate, acting via food availability, have discernible impacts on the regulation of this population. Capelin biomass and timing of spawning were well explained by a regime shift and seasonal sea ice dynamics, a key determinant of the pelagic spring bloom. Our findings are important for the development of ecosystem approaches to fisheries management and raise questions on the potential impacts of climate change on the structure and productivity of this marine ecosystem.