Determining changes in the water level of lakes is essential in terms of flood control, water resource management, economic development, water-supply planning sustainability, and the sustainability of the ecosystem. Trend analysis is one of the most commonly used tools for detecting changes in the hydrological time series such as lake levels, precipitation and temperature. Trend analyses of meteorological variables and groundwater levels (baseflow components) are crucial toward the assessment of long-term changes in lake levels. This study aims to investigate the trend of long-term change in lakes (Lake Tuz and Lake Beyşehir) and sinkholes (Timraş and Kızören) in the Konya Closed Basin in Turkey. Changes in these lakes and sinkholes were examined along with changes in precipitation and groundwater trends representing the climate in the region. With the assistance of Thiessen polygons, precipitation stations, which affect the lakes and sinkholes, were determined. Several statistical tests exist that help determine the significance of hydrological trends over time. These tests are divided into two categories: parametric and nonparametric. In this study, the non parametric Innovative Sen trend test, the Modified Mann–Kendall trend test, and the parametric Linear Trend test were used. As a result of the trend analysis, it was observed that the water levels of Kızören and Timraş sinkholes decreased over time, and the water levels of Tuz Gölü and Beyşehir lakes increased over time. These results are supported by the trends of precipitation data and groundwater level data of the stations determined by the Thiessen polygons and sub-basin boundaries.