Abstract The response of the oceanic surface layer to atmospheric shallow convection is explored using realistic atmospheric large eddy simulations coupled with an oceanic 1D model with high vertical resolution. The effects of cloud shading, rain, and enhanced heat loss due to gust fronts on the edge of cold pools and their interactions are investigated in a case study of the Cooperative Indian Ocean Experiment on Intraseasonal Variability/Dynamics of the Madden–Julian Oscillation experiment in the tropical Indian Ocean, during a suppressed phase of the Madden–Julian Oscillation. Conditions of low surface wind and strong solar heating result in diurnal warming of the oceanic surface of 2 °C over a depth of 1 m. Analysis of specific periods covering the diurnal cycle shows the contrasting effects of cloud shading, rain, and turbulent heat fluxes under the cold pools on the sea temperature at the surface and below. On the one hand, decreasing the solar radiation (cloud shading) results in slight cooling extended horizontally and penetrating down to 1–2 m depth, depending on the time of the day. On the other hand, turbulent heat fluxes enhanced up to 300 Wm by gusts and freshwater lenses due to rain act together and more locally. They isolate and strongly cool a thin inner layer at the surface, which eventually destabilizes the surface layer and propagates the cooling downward. The exact relative part and efficiency of these processes depend on the time evolution of the thermal stratification and vertical turbulent mixing in the oceanic upper layer. Surface cooling of up to 0.5 °C may occur in a few tens of minutes and last for several hours, significantly mitigating the effects of diurnal warming over large extents.