Understanding the variability and predominant drivers of water level fluctuations in large water bodies is critical for the development of proactive mitigation plans in the nearshore zone. Here, for the first time, we reconstructed the individual and collective influence of the Atlantic Multi-decadal Oscillation, Pacific Decadal Oscillation, region 3.4 of El Niño-Southern Oscillation, and North Atlantic Oscillation on Lake Huron-Michigan’s water budget components, including water levels, over-lake precipitation, evaporation, runoff, and river flow rates over a 115-year period. Conducting wavelet spectral analysis on the reconstructed impact of large-scale climate oscillations revealed the emergence of quasi-periodic and non-stationary fluctuations along with frequency shifts in hydrological variables, highlighting their increasingly stronger signature on water levels after 1980. After removing the atmospheric teleconnection effects, the residual hydrological time series provided evidence of gradual changes in runoff and river flow rates and their relationships with precipitation, reflecting the effects of intensifying anthropogenic activities on the regional water cycle over the past decades. Considering the uncertainty pertaining to the magnitude and frequency of atmospheric teleconnections in a changing climate, the findings of our study can offer a new perspective in our understanding of the drivers of water level variability along the shoreline and/or the navigability of shallow waters in the Great Lakes.