A method based on UPLC-MS/MS (ultraperformance liquid chromatography—tandem mass spectrometry) was optimized for the analysis of a broad set of antibiotics and their metabolites in surface and wastewaters after their preconcentration by solid-phase extraction (SPE). The method was applied to the monitoring of the river basin of the POCTEFA (Interregional Programme Spain-France-Andorra) territory (Spain and France) in frame of a sampling campaign (2020–2021) including 40 sampling points, 28 of them corresponding to surface waters and 12 to wastewaters. In total, 21 antibiotics belonging to different families, i.e., ciprofloxacin, sulfamethoxazole, trimethoprim, azithromycin, and their metabolites were detected. A higher overall antibiotic contamination was observed in the Spanish part of the POCTEFA territory. Several metabolites of the target antibiotics, some of them supposed to be more toxic than their parent compounds, were identified in the entire sampling network. Fluoroquinolones and sulfamethoxazole, as well as their metabolites, presented the highest detection frequency both in wastewaters and surface waters, and, consequently, should be considered as target compounds in the monitoring of the water resources of the POCTEFA territory.