The one-dimensional lake model GLM was used to simulate the ice and stratification dynamics of two small lakes within Moscow City, Russia – lakes Beloe and Svyatoe of the Kosino Lake group. The model was calibrated on observation data from 2021–2023, and the significant trends of the lakes’ thermal and mixing regime were calculated based on the model run for the period of 1983–2023. Some of the most distinct changes are associated with ice phenology, as both lakes lose ice cover at 4.4–5.0 days/decade. The length of the stratified period does not significantly change, but the stability of stratification in dimictic Lake Beloe is increasing. Both lakes have experienced an increase in mean surface water temperature over the year between 0.22–0.26 °C/decade, which is two times lower than the observed trend in the local air temperature. In polymictic Lake Svyatoe, bottom water temperature also increases at a maximum of 0.65 °C/decade. The fastest changes in ice phenology, water temperature and stratification occurred before 2013, while in the last decade most parameters have stabilized, despite the growing intensity of climate warming. This might demonstrate how the lakes are compensating for some of the climate signal.