Small lakes are ecosystems highly impacted by climate change. Here, the thermal regime of a small, shallow lake over the past six decades was reconstructed via 3D modelling. Significant changes were found: strong water warming in spring and summer (0.7 °C/decade) as well as increased stratification and thermal energy for cyanobacteria growth, especially in spring. The strong spatial patterns detected for stratification might create local conditions particularly favourable to cyanobacteria bloom.