Oxygen deficiency is a major environmental problem deteriorating seafloor habitats especially in the coastal ocean with large human impact. Here we apply a wide set of chemical and physical analyses to a 1500-year long sediment record and show that, although long-term climate variability has modulated seafloor oxygenation in the coastal northern Baltic Sea, the oxygen loss over the 20th century is unprecedentedly severe, emphasizing the need to reduce anthropogenic nutrient input in the future.