Migratory species with disjunct and localized breeding distributions, including many colonial marine birds, pose challenges for management and conservation as their dynamics are shaped by both broad oceanographic changes and specific factors affecting individual breeding colonies. We compare six colonies of the declining Leach's storm-petrel, Hydrobates leucorhous, across their core range in Atlantic Canada using standard capture-mark-recapture methods to estimate annual survival of individually marked populations of breeding adults. Over the period analysed (5–20 years per colony; 2003–2022), mean annual survival varied among colonies (0.81–0.88) and annually (process error σ ranging from 0.01 to 0.09), though annual fluctuations were not synchronous across colonies. Two colonies with limited natural predation showed higher survival, and there was a decline in survival with increasing colony-specific total mercury burden. Our work shows that colony-specific pressures and regional contaminant burdens are potentially important contributors to current population declines, and highlights the importance of monitoring demographic rates at multiple sites for species that congregate at key life-history stages.