Offshore Antarctic polynyas—large openings in the winter sea ice cover—are thought to be maintained by a rapid ventilation of deep-ocean heat through convective mixing. These rare phenomena may alter abyssal properties and circulation, yet their formation mechanisms are not well understood. Here we demonstrate that concurrent upper-ocean preconditioning and meteorological perturbations are responsible for the appearance of polynyas in the Weddell Sea region of the Southern Ocean. Autonomous profiling float observations—collected in 2016 and 2017 during the largest polynyas to form near the Maud Rise seamount since 1976—reveal that the polynyas were initiated and modulated by the passage of severe storms, and that intense heat loss drove deep overturning within them. Wind-driven upwelling of record strength weakened haline stratification in the upper ocean, thus favouring destabilization in 2016 and 2017.