Long-term hydroclimate variability recorded in lake sediments from Estonia provide information about environmental changes in northern Europe during the Holocene. Lake Pangodi is a semi-closed basin lake in southern Estonia with a large surface area to volume ratio, making it sensitive to effective moisture balance (precipitation minus evapotranspiration), which is recorded as changes in the lake level. Here we conducted a ground penetrating radar (GPR) survey, sedimentological analyses, radiometric dating and lake level modeling study to identify periods of lake-level high- and low-stands. The radiocarbon-dated sedimentary stratigraphic features on our radargram support the model results, suggesting that Lake Pangodi formed at ∼12.8 ka. The water levels were likely variable during the early Holocene, and the comparison of Lake Pangodi sediment facies and the lake level model show relatively stable lake water depth between ∼9.8 ka and ∼2.4 ka, and an increase towards modern. A notable reduction in lake levels occurred between ∼8.2 and ∼7.7 ka, likely due to a significantly reduced precipitation-evaporation balance. Our middle Holocene reconstruction suggests water column depths nearly 2.0 m lower than modern. This aligns with the results from studies conducted in the Baltic region, yet contrasts those from Scandinavia, suggesting different hydroclimate driving mechanisms during the Holocene variations in hydrogeological regimes. Our model detected the most abrupt rise of 1.7 m in water levels between ∼1.5 and ∼1.3 ka. This study highlights the need to develop proxies from single lake basins combining multiple methods for a better spatiotemporal resolution of paleo-hydrological changes.