Climate change affects physical and biogeochemical processes in lakes. We show significant increases in surface-water temperature (~ 0.5 °C decade-1; > 0.2% year-1) and wave power (> 1% year-1; the transport of energy by waves) associated with atmospheric phenomena (Atlantic Multidecadal Oscillation and Multivariate El Niño/Southern Oscillation) in the month of August between 1980 and 2018 in the Laurentian Great Lakes. A pattern in wave power, in response to extreme winds, was identified as a proxy to predict interbasin coupling in Lake Erie. This involved the upwelling of cold and hypoxic (dissolved oxygen < 2 mg L-1) hypolimnetic water containing high total phosphorus concentration from the seasonally stratified central basin into the normally well-mixed western basin opposite to the eastward flow. Analysis of historical records indicate that hypoxic events due to interbasin exchange have increased in the western basin over the last four decades (43% in the last 10 years) thus affecting the water quality of the one of the world's largest freshwater sources and fisheries.