Water temperature and the alternation of stratification and mixing count amongst key drivers of lake ecology. Reliable long time-series of water temperature are rare. Here, we investigated how a numerical model can fill the gaps in heterogeneous time-series and make it possible to identify a significant trend in the lake thermal regime. We computed the mean water temperature and the Schmidt stability, an indicator of the stratification strength, in a deep and well-stratified lake (Lake Bourget, France), between 1976 and 2008. We first used temperature measurements and then a one-dimensional vertical model, which we describe here. The model performs as well as the best existing models. During the 1976-2008 periods, whereas no statistically significant trend came out of the measurements, we found in the simulation results an increase of 0.12 °C per decade in the water temperature and of 5.9 days per decade in the stratification duration. This shows that the temperature history of a lake can be reconstructed and a reliable long-term trend computed when weather data and a calibrated temperature model are available. Our results also suggest that different local climatic influences cause a slower warming in this lake of the south-western Alps than in other sub-alpine lakes.