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Abstract Superoxide is a reactive oxygen species that is influential in the redox chemistry of a wide range of biological processes and environmental cycles. Using a novel in situ sensor we report the first water column profiles of superoxide in the Baltic Sea, at concentrations higher than previously observed in other oceans. Our data revealed consistent peaks of superoxide (2.0–15.1 nM) in dark waters just below the mixed layer. The oxic waters, low metal concentrations, and lack of sunlight imply that the peak is likely of biological origin. Several profiles displayed a concomitant dip in dissolved oxygen mirroring this superoxide peak, strongly suggesting a link between the two features. The magnitude and distribution of superoxide observed warrants re‐evaluation of the most relevant sources and controls of superoxide in seawater. Locally, these high concentrations of superoxide may create environments conducive to reactions with trace metals and organic matter and present an overlooked sink of oxygen in the Baltic Sea.