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This dataset contains data that was collected for the HELCOM report on Pharmaceuticals in the Baltic sea (http://helcom.fi/Lists/Publications/BSEP149.pdf). UNESCO and HELCOM, 2017 (to be published). Status report on pharmaceuticals in the Baltic Sea region. Baltic Sea Environment Proceedings No. 149. Partly funded by Interreg Baltic Sea Region (EU Strategy support through Policy Area Hazards). Financial support was provided by Interreg Baltic Sea Region, United Nations Educational, Scientific and Cultural Organization (UNESCO) and Swedish International Development Cooperation Agency (SIDA). The report was prepared as a case study for the UNESCO-IHP International Initiative on Water Quality (IIWQ) UNESCO project: Emerging Pollutants in Wastewater Reuse in Developing Countries. Case Studies on Emerging Pollutants in Water and Wastewater. The dataset contains compound name, species, biota matrix, concentrations and whether compound has been detected in the sample. This dataset presents a compilation of concentrations and effects of pharmaceuticals in the Baltic Sea marine environment based on data collected by all Baltic Sea states via working groups of the Helsinki Commission, HELCOM. Data collected between the years 2003 to 2014, from coastal, open sea and transitional areas, was received from Denmark, Estonia, Finland, Germany, Poland and Sweden. • 4600 individual data posts were included in the complete data set • 167 different pharmaceuticals have been measured and 74 of these were found in at least one of the sampling matrices (water, sediment, biota) • 51 different pharmaceuticals have been detected in water (of 148 measured) • 9 different pharmaceuticals have been detected in sediment samples (of 25 measured) • 35 different pharmaceuticals have been detected in biota samples (of 116 measured) • Pharmaceuticals from all drug classes were detected See HELCOM BSEP 149 report chapter ”3. Data collection methodology and data availability” for further information.