This report describes the contamination by pharmaceuticals and the environmental risks associated with their environmental levels in the Baltic Sea Region. Data were collected within the three-year project Clear Waters from Pharmaceuticals (CWPharma) funded by the EU’s Interreg Baltic Sea Region Programme. Sampling was performed in the river basin districts of Vantaanjoki in Finland, Pärnu in Estonia, Lielupe and Daugava in Latvia, Vistula in Poland, Warnow-Peene in Germany and Motala ström in Sweden. Analyses were performed on surface water, coastal water, sediment and soil that was fertilized with sewage sludge or manure. Analyses were also performed on emissions from municipal wastewater treatment plants, hospitals, pharmaceutical manufacturing facilities, landfills, and fish and livestock farms. In total, the study covered 13 365 data points from 226 samples as well as collection of human and veterinary consumption data of selected active pharmaceutical ingredients (APIs). Samples were screened for up to 80 APIs, representing antibiotics, antiepileptics, antihypertensives, asthma and allergy medications, gastrointestinal disease medications, hormones, metabolic disease medications, non-steroidal anti-inflammatory drugs (NSAIDs) and analgesics, other cardiovascular medicines, psychopharmaceuticals, veterinary medicines and caffeine. The measured APIs were selected based on analytical capacity, consumption rates, identified data gaps and potential environmental risks. Literature and databases were screened for ecotoxicological information. Acute toxicity tests were performed for two APIs, nebivolol and cetirizine, for which ecotoxicological data were lacking. Measured environmental concentrations were compared with predicted no-effect concentrations (PNEC) to assess environmental risks of the selected APIs.