Long-term changes in air and water temperatures and the resulted stratification phenomena were observed for Soyang Lake (SY), Paldang Lake (PD), Chungju Lake (CJ), and Daecheong Lake (DC) in South Korea. Non-parametric seasonal Kendall and Mann-Kendall tests, Sen slope estimator, and potential energy anomaly (PEA) were applied. The lake surface water temperatures (LSWTs) of SY and DC increased at the same rate (0.125 °C/y), followed by those of CJ (0.071 °C/y) and PD (0.06 °C/y). Seasonally, the LSWT increase rates for all lakes, except PD, were 2–3 times higher than the air temperature increase rates. The lake stratification intensity order was similar to those of the LSWT increases and correlations. SY and DC displayed significant correlations between LSWT (0.99) and PEA (0.91). Thus, the LSWT significantly affected stratification when the water temperature increased. PD demonstrated the lowest correlation between LSWT and PEA. Inflow, outflow, rainfall, wind speed, and retention time were significantly correlated, which varied within and between lakes depending on lake topographical, hydraulic, and hydrological factors. Thus, hydraulic problems and nutrients should be managed to minimize their effects on lake water quality and aquatic ecosystems because lake cyanobacteria can increase as localized water temperatures increase.