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The objective of this study is to analyze the temporal variability in water levels of Lake Mégantic (27.4 km2) during the period 1920–2020 in relation to anthropogenic and natural factors on the one hand, and its impact on the intensity and frequency of heavy flooding (recurring floods ≥ 10 years) of the Chaudière River of which it is the source, on the other hand. The application of four different Mann–Kendall tests showed a significant decrease in lake water levels during this period. The Lombard test revealed two breaks in the average daily maximum and average water levels, but only one break in the average daily minimum water levels. The first shift, which was smoothed, occurred between 1957 and 1963. It was caused by the demolition in 1956 of the first dam built in 1893 and the significant storage of water in the dams built upstream of the lake between 1956 and 1975. The second shift, which was rather abrupt, occurred between 1990 and 1993. It was caused by the voluntary and controlled lowering of the lake’s water levels in 1993 to increase the surface area of the beaches for recreational purposes. However, despite this influence of anthropogenic factors on this drop in water levels, they are negatively correlated with the global warming climate index. It is therefore a covariation, due to anthropogenic factors whose impacts are exerted at different spatial scales, without a physical causal link. However, the winter daily minimum water levels, whose temporal variability has not been influenced by anthropogenic activities, are positively correlated with the NAO and AO indices, but negatively with PDO. Finally, since the transformation of Lake Mégantic into a reservoir following the construction of the Mégantic dam in 1893 and 1973 to control heavy flooding in the Chaudière River, all recurrent floods ≥ 10 years have completely disappeared in the section of this river located downstream of Lake Mégantic. However, the disappearance of these floods and the drop in water levels of Lake Mégantic have not significantly impacted the stationarity in the flow series of the Chaudière River since 1920.