Phosphorus is an essential element for life and its cycling strongly impact primary production. Here, we present a dataset of sediment-water fluxes of dissolved inorganic phosphorus from the Baltic Sea, an area with a long history of eutrophication. The fluxes were measured in situ with three types of benthic chamber landers at 59 stations over 20 years. The data show clear spatial patterns and will be important for marine management and studies on mechanisms in benthic phosphorus cycling.