Historically, phosphorus has been considered the limiting nutrient for primary production in the northern Baltic Sea, whereas further south in the Baltic Proper nitrogen is the limiting nutrient. In this study, we investigated the nutrient distribution during the past 30 years using Swedish and Finnish monitoring data. The results show comprehensively for the first time that the entire Bothnian Sea has switched to nitrogen limitation and that the Bothnian Bay is rapidly heading towards similar conditions. This is due to increasing inorganic phosphorus concentrations, possibly resulting from phosphorus rich water inflowing from the Baltic Proper. Inorganic nitrogen concentrations decrease or are unchanged. The increase of phosphorus led to increased primary production and, in the Bothnian Sea, to increased occurrence of filamentous cyanobacteria. The resulting shift emphasizes the need to revise management strategies of these basins, where treating both basins for phosphorus and nitrogen is advisable.