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The present dataset provides data on the pharmaceutically active compounds (PhACs) concentrations measured in the Danube and the drinking water abstraction wells (DWAW) in the Budapest region. Grab samples were collected during five periods. One hundred and seven water samples from the Danube and ninety water samples from the relevant DWAWs were analyzed to quantify physical-chemical parameters, trace element concentrations, and one hundred and eleven PhACs, including pharmaceutical derivatives, illicit drugs, and alkaloids. The ion concentrations were measured using dual channel ion chromatography, spectrophotometric and titrimetric methods, and inductively coupled plasma mass spectrometry. PhACs concentrations were measured after solid-phase extraction applying supercritical fluid chromatography coupled with tandem mass spectrometry. Fifty-two PhACs were quantified in the Danube, and ten PhACs were present in >80% of the samples. Whereas thirty-two PhACs were quantified in the DWAWs. The present dataset is useful for further comparisons and meta-analyses.