Trend analyses of meteorological variables play an important role in assessing the long-term changes in water levels for sustainable management of shallow lakes that are extremely vulnerable to climatic variations. Lake Mogan and Lake Eymir are shallow lakes offering aesthetic, recreational, and ecological resources. Trend analyses of monthly water levels and meteorological variables affecting lake levels were done by the Mann-Kendall (MK), Modified Mann-Kendall (MMK), Sen Trend (ST), and Linear trend (LT) methods. Trend analyses of monthly lake levels for both lakes revealed an increasing trend with the Mann-Kendall, Linear, and Sen Trend tests. The Modified Mann-Kendall test results were statistically significant with an increasing trend for Eymir lake levels, but they were insignificant for Mogan lake due to the presence of autocorrelation. While trend analyses of meteorological variables by Sen Test were significant at all tested variables and confidence levels, Mann-Kendall, Modified Mann-Kendall, and Linear trend provided significant trends for only humidity and wind speed. The trend analyses of Sen Test gave increasing trends for temperature, wind speed, cloud cover, and precipitation; and decreasing trends for humidity, sunshine duration, and pan evaporation. These results show that increasing precipitation and decreasing pan evaporation resulted in increasing lake levels. The results further demonstrated an inverse relationship between the trends of air temperature and pan evaporation, pointing to an apparent "Evaporation Paradox", also observed in other locations. However, the increased cloud cover happens to offset the effects of increased temperature and decreased humidity on pan evaporation. Thus, all relevant factors affecting pan evaporation should be considered to explain seemingly paradoxical observations.