High-resolution numerical simulations of the Baltic Sea reveal that fine-scale features known as submesoscales are widespread in the deeper layers of the basin, especially near its boundaries. These features are linked to strong mixing and, in this wind-driven system, are found to intensify during storms, with wind reversals shifting the location of mixing hotspots. Our results suggest that storm-modulated submesoscales may be important in other wind-driven coastal seas and lakes.