Delays in waterfowl autumn migration have been widely reported by hunters and ornithologists throughout North America. The implications of such delays are vast, with potential effects on the efficacy of population management, reduced social and economic opportunities, and reduced resource availability by overuse and over-grazing in key staging areas. In this study, we tested for changes in autumn migration timing for six abundant species of dabbling ducks in southern Ontario, Canada. We applied generalized linear mixed models to test for effects of year and climate indices El Niño Southern Oscillation (ENSO) and North Atlantic Oscillation (NAO) on the Julian date of peak abundance as observed during aerial surveys conducted throughout the lower Great Lakes. Our analyses revealed delays of 11–18 days between 1968 and 2011 for four of six focal species: mallard, American black duck, American wigeon and gadwall. La Niña and El Niño events had no effect on migration timing for American black duck, American green-winged teal or American wigeon, while an increase in the annual NAO index resulted in a delayed migration for American wigeon. There was an NAO:ENSO interaction for mallard and gadwall migration; an increase in NAO advanced peak migration dates during La Niña events. However, an increase in NAO delayed migration for gadwall during the neutral phase of the ENSO and delayed migration for both species during El Niño events. Blue-winged teal and American green-winged teal showed no change in migration timing. Given that climate forecasts indicate continued positive-value phases, the autumn migrations for mallard, American black duck, gadwall and American wigeon may become increasingly delayed. Wildlife managers should use all available data, including from standardized aerial surveys, citizen science and climate models to inform and direct adaptive population management, hunting regulations, wildlife emergency response and habitat conservation.