In our article “Ecological risk assessment of pharmaceuticals in the transboundary Vecht River (Germany/Netherlands)” (https://doi.org/10.1002/etc.5062) we defined unique ecological risk profiles for surface water concentrations of pharmaceuticals in the Vecht River. Therefore, it was necessary to collect up-to-date ecotoxicity effect data. The present dataset provides the aquatic toxicity data used to determine predicted environmental concentrations (PNEC) for a selection of pharmaceuticals. A wealth of effect data from scientific literature, databases and other sources was collected, cleaned and harmonized. The dataset was created with particular focus on 8 pharmaceuticals (carbamazepine, ciprofloxacin, cyclophosphamide, diclofenac, erythromycin, 17α-ethinylestradiol, metformin, and metoprolol), although data on more than 220 substances from scientific literature were also extracted in the process. Details on the character and the purpose of the research, the nature of the data, the way the data were collected, processed and analysed are provided.