The effectiveness of marine conservation areas are influenced by the structure of the food webs they encompass, including the population dynamics of potentially important forage species that occupy trophic positions between those of zooplankton and higher trophic levels. Capelin is a key forage species for marine mammals, seabirds, and fish in the Saguenay-St. Lawrence Marine Park (SSLMP, Canada), yet knowledge on its population dynamics is incomplete. In particular, the natal sources sustaining this critical forage species within the conservation area remain unknown. Otolith microchemistry as an index of natal habitat was investigated, including measures of boron, barium, iron, magnesium, manganese, and strontium over the protracted spawning season of capelin. Otolith microchemistry indicated that the principal natal source of 1+ capelin found within the SSLMP was located in the St. Lawrence estuary, outside the conservation area boundaries. To ensure the sustainability key forage species within the conservation area, larger scale long-term management strategies are necessary to encompass ecological processes related to capelin that extend beyond the conservation area boundaries.