This study provides unique data on temperature and salinity anomalies between the skin layer (upper first millimetre) and a depth of 100 cm during abrupt meteorological changes—that is, shifts in air temperature, wind speed, precipitation, and heat fluxes. We determined how these abrupt meteorological changes forced the anomalies and altered the conditions at the air–sea boundary layer during three events monitored by an autonomous surface vehicle. Two events were observed in the harbour of Bremerhaven and one event in the North Sea. The skin layer, which covers the upper millimetre of the sea surface, interacts with the atmosphere, including heat, gas, and freshwater fluxes. The characteristics of the skin layer regulate the exchange of heat and gases between the atmosphere and the ocean. Global climate change increases extreme weather events, highlighting the need for observations during abrupt shifts to better estimate heat flux changes. However, there is a lack of small-scale mechanistic understanding of these fluxes, especially under abrupt meteorological changes, due to observational challenges during stormy conditions in the open sea. Here, we show that the skin layer instantly reacts to abrupt meteorological changes. The average temperature change in the skin layer was almost 50 % higher than that at a depth of 100 cm. An abrupt change in meteorological conditions, shifting the net heat flux from positive to negative, can turn a warm skin layer into a cooler layer compared with the 100 cm depth. The effect of abrupt meteorological changes, including freshwater fluxes, on salinity anomalies was less pronounced in the harbour than in the North Sea event. The current velocities showed that changes in wind direction could alter the surface current direction, and that the backscatter signal consistently reflects wind-induced mixing, with higher backscatter observed during increased wind conditions. This study reveals the complex relationships between atmospheric conditions and oceanic responses and provides valuable information for understanding air–sea interactions and their implications for climate dynamics.