Thermal dynamics of lakes has a key role in chemical and biological processes in lakes including nutrient distributions and phytoplankton growth. Applications of hydrodynamic models to lakes can provide insights into possible future alterations in thermal dynamics induced by climate change. In this study, we present the calibration and validation of the newest version of the open-source hydrodynamic model GLM (General Lake Model) to the dimictic Lake Ammersee, located in south-east Germany. The simulation of lake water temperatures for the calibration period revealed an overall root mean square error of 0.65 °C and a mean error of 0.08 °C. The seasonal stratification pattern and the annual thermal structure of this dimictic lake were reproduced by the model. The model simulated the presence of winter ice cover for the only year out of 8 years simulated, when ice cover was observed. Elevated lake water temperatures were also reproduced in model simulations during a period in 2003 of unusually high air temperatures. Statistical analysis of the model calibration results for Lake Ammersee indicates a fit comparable to or better than most other well-established hydrodynamic models and provides an opportunity for continuous simulations through periods of ice cover. Our results indicate a major improvement in GLM compared with earlier model versions and demonstrate the applicability of GLM for limnophysical studies, particularly for altered forcing conditions such as climate change.