Hypoxia (oxygen concentrations of <2 ml/L) and so-called “dead zones” are a growing concern in coastal marine environments. The Baltic Sea is a shelf sea that is highly sensitive to hypoxia, and may serve as a laboratory for studying the interplay between natural and anthropogenic forcing of redox conditions in the global coastal zone. Past occurrences of hypoxia in the Baltic Sea have been shown by previous studies, but high-resolution, quantitative reconstructions of past hypoxia intensity are lacking. Here we present bulk sediment geochemical records from the deep basins of the Baltic Sea that show multicentennial oscillations during intervals of past hypoxia, suggesting rapid alternations between hypoxic and relatively oxic conditions. While the onset of past hypoxic events was likely forced by climatic variability, these events intensified and terminated rapidly due to feedbacks in the phosphorus (P) cycle. The modern intensity of hypoxia is similar to several past events, suggesting that hypoxia in the Baltic Sea has a maximum potential intensity. However, using ultrahigh-resolution laser ablation–inductively coupled plasma–mass spectrometry scanning of sediment blocks, we show that modern hypoxia intensified more rapidly than any past event. This confirms the role of anthropogenic nutrient loading in driving this system into its current hypoxic state.