These data relate to the analysis of emerging contaminants in water. Surface water samples were analyzed using targeted methods for the simultaneous determination of pharmaceuticals, hormones, pesticides, and other compounds by liquid chromatography–triple quadrupole mass spectrometry (LC–MS/MS). Groundwater samples impacted by aqueous film-forming foams (AFFF) were analyzed using a suspect-screening approach for per- and polyfluoroalkyl substances (PFAS) by liquid chromatography–high-resolution mass spectrometry with an Orbitrap analyzer (LC–HRMS). The dataset includes quantitative concentration data from targeted analyses and results from suspect screening.