A highly temporally and spatially resolved measurement campaign was conducted over a one-year period to analyze water samples for a total of 35 pharmaceuticals, pesticides and UV-filters. Between spring 2022 and spring 2023, surface water samples were collected twice a week at 14 sites at the Warnow estuary and its adjacent areas in Rostock, Germany, as part of the OTC-Genomics sampling campaign. The sampling area included one upstream freshwater site before the river enters the estuary, seven sampling sites along the estuary - surrounded by the urban area of Rostock - and six sites along the Baltic coastline. Sampling was conducted every Monday and Thursday, always three hours after sunrise. After enrichment with solid phase extraction, 1307 samples were analyzed using liquid chromatography–tandem mass spectrometry. Additional to the dataset included here, the same samples were analyzed for prokaryotic and eukaryotic community composition (16S and 18S rRNA gene amplicon sequencing), cell abundances (flow cytometry), and physico-chemical environmental parameters.

"#" before value means data point is (LOD+LOQ)/2 because LOD < data point < LOQ (LOD = limit of detection, LOQ = limit of quantification); "<" means less than