In lakes and reservoirs, physical processes control temperature dynamics and stratification, which are important determinants of water quality. In large lakes, even extensive monitoring programs leave some of the patterns undiscovered and unresolved. Lake models can complement measurements in higher spatial and temporal resolution. These models require a set of driving data, particularly meteorological input data, which are compulsory to the models but at many locations not available at the desired scale or quality. It remains an open question whether these meteorological input data can be acquired in a sufficient quality by employing atmospheric models. In this study, we used the European Centre for Medium-Range Weather Forecasts' (ECMWF) ERA-Interim atmospheric reanalysis data as meteorological forcing for the three-dimensional hydrodynamic General Estuarine Transport Model (GETM). With this combination, we modelled the spatio-temporal variation in water temperature in the large, shallow Lake Chaohu, China. The model succeeded in reproducing the seasonal patterns of cooling and warming. While the model did predict diurnal patterns, these patterns were not precise enough to correctly estimate the extent of short stratification events. Nevertheless, applying reanalysis data proved useful for simulating general patterns of stratification dynamics and seasonal thermodynamics in a large shallow lake over the year. Utilising reanalysis data together with hydrodynamic models can, therefore, inform about water temperature dynamics in the respective water bodies and, by that, complement local measurements.