The eutrophication of shallow lakes in densely populated areas hinders their usages, including the very demanded outdoor activities and bathing. The main disturbance is due to the proliferation of phytoplankton, especially of toxic species. Our objective is to predict the starting point and the expansion of phytoplankton proliferations, and more precisely to distinguish the respective impacts of nutrient resuspension due to wind and of the external nutrient loading by stormwater. Our study site is Lake Créteil, France, a former sand pit and now eutrophic lake of 40 ha and of mean depth 4.5 m. The experimental and modelling activities of the site are supported by KIC-Climate ‘Blue Green Dream’ and R2DS ‘PLUMMME’ projects. Meteorological variables (solar radiation, wind speed and direction, air temperature, humidity and rainfall), water velocity profiles, water temperature at different depths and chlorophyll-a concentration at the same depths have been measured in the deep region (5.5 m) at the centre of the lake. Water temperature and chlorophyll-a concentration have also been measured at two other locations, North and South of the centre, and at several depths. All data have been recorded every 30 s. The flow discharge and nutrient concentrations (total phosphorus, phosphate and nitrate) have also been measured in the stormwater inlet during rainfall periods. Maximum horizontal differences of up to 1 °C in water temperatures have been measured at the beginning of thermal stratification periods, when phytoplankton blooms usually start. The 3D hydrodynamic model Delft3D-FLOW has been calibrated and validated during periods of thermal stratification and full mixing of several weeks. Water temperatures are well reproduced by the model (RMSE = 0.2 °C), as well as water velocities (RMSE = 0.6 cm/s) and also the main modes of internal waves. Simulation results have shown favourite regions for potential nutrient resuspension during full mixing but also during internal wave activity, by locating high bottom shear stress values. In conclusion we discuss the recent advances performed in calibration of the linked water quality model DELWAQ, which should allow us to track the starting point and the expansion of observed phytoplankton proliferations.