Abstract. Small, shallow lakes represent the majority of inland freshwater bodies. However, the effects of climate change on such ecosystems have rarely been quantitatively addressed. We propose a methodology to evaluate the thermal response of small, shallow lakes to long-term changes in the meteorological conditions through model simulations. To do so, a 3D thermal-hydrodynamic model is forced with meteorological data and used to hindcast the evolution of an urban lake in the Paris region between 1960 and 2017. Its thermal response is assessed through a series of indices describing its thermal regime in terms of water temperature, thermal stratification, and potential cyanobacteria production. These indices and the meteorological forcing are first analysed over time to test the presence of long-term monotonic trends. 3D simulations are then exploited to highlight the presence of spatial heterogeneity. The analyses show that climate change has strongly impacted the thermal regime of the study site. Its response is highly correlated with three meteorological variables: air temperature, solar radiation, and wind speed. Mean annual water temperature shows a considerable warming trend of 0.6 ∘C per decade, accompanied by longer stratification and by an increase in thermal energy favourable to cyanobacteria proliferation. The strengthening of thermal conditions favourable for cyanobacteria is particularly strong during spring and summer, while stratification increases especially during spring and autumn. The 3D analysis allows us to detect a sharp separation between deeper and shallower portions of the basin in terms of stratification dynamics and potential cyanobacteria production. This induces highly dynamic patterns in space and time within the study site that are particularly favourable to cyanobacteria growth and bloom initiation.