Abstract In the Southern Ocean, upper ocean processes are important for water column stability, affecting air‐sea‐ice fluxes. Eddies can facilitate exchange with deeper layers, affecting heat and salt fluxes, though observations are lacking. New novel observations from an acoustically tracked profiling float, trapped within an eddy for 6 months, present the first direct vertical heat flux estimates due to eddy‐sea ice interactions. These observations revealed an increase in wintertime salt and heat fluxes to the upper ocean, resulting in a reduced mixed layer thickness at the end of winter and possible anomalous winter sea ice melt. Observational estimates of salt and heat fluxes were compared with those derived from eddies identified in a high‐resolution numerical simulation showing similar results. With the event based nature of eddies, this introduces highly variable salt and heat fluxes across the Weddell Sea, potentially impacting Winter Water evolution, spring time melt, and deep ocean convection.