We compared changes in body condition (relative weight) and mercury concentrations ([Hg]) in two species of coregonid fish (lake herring Coregonus artedi, lake whitefish C. clupeaformis) among discrete populations in Ontario between 1967 and 2006. Temporal comparisons among populations were made to determine whether 1) the establishment of Bythotrephes longimanus had affected coregonid populations, or 2) if changes in body condition or [Hg] were related to regional differences in the degree of climate change during the time period investigated. Climate data from northwestern, northeastern and southern Ontario showed a general warming trend in all regions over the period of study. However, greater temporal changes in climate were observed in the northwest where growing degree days >5°C (GDD) increased and precipitation declined over the study period compared with relatively little change in southern or northeastern Ontario. Correspondingly, northwestern Ontario coregonid populations demonstrated significantly greater declines in body condition relative to those from northeastern or southern Ontario. Declines in [Hg] of both species were also greater among northwestern populations compared with those from northeastern or southern Ontario but only significantly so for lake herring. These declines were independent of the invasion of non-native Bythotrephes, and declines in [Hg] were opposite predictions based on the hypothesis that Bythotrephes invasion lengthened aquatic food chains. Based on our findings and further evidence from the literature, we propose that warming regional climates are capable of contributing to declines in both condition and [Hg] of fishes. Because fish condition affects both reproductive success and overwinter survival, observed condition declines of the magnitude reported here could have profound implications for the structure of future aquatic ecosystems in a warming climate.