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Ice-sheet mass loss is one of the clearest manifestations of climate change, with Antarctica discharging mass into the ocean via melting or through calving. The latter produces icebergs that can modify ocean water properties, often at great distances from source. This affects upper-ocean physics and primary productivity, with implications for atmospheric carbon drawdown. A detailed understanding of iceberg modification of ocean waters has hitherto been hindered by a lack of proximal measurements. Here unique measurements of a giant iceberg from an underwater glider enable quantification of meltwater effects on the physical and biological processes in the upper layers of the Southern Ocean, a region disproportionately important for global heat and carbon sequestration. Iceberg basal melting erodes seasonally produced winter water layer stratification, normally forming a strong potential energy barrier to vertical exchange of surface and deep waters, while freshwater run-off increases and shoals near-surface stratification. Nutrient-rich deeper waters, incorporating meltwater loaded with terrigenous material, are ventilated to below this stratification maxima, providing a potential mechanism for alleviating critical phytoplankton-limiting components. Regional historical hydrographic data demonstrate similar stratification changes during the passage of another large iceberg, suggesting that they may be an important pathway of aseasonal winter water modification.