Abstract The widespread occurrence of antibiotics in the environment may exert a negative impact on wild organisms. In addition, they can become environmental reservoirs, through the ingestion of food or contaminated water, and vectors for antibiotic-resistant bacteria. This fact is even more important in migratory birds that can promote their dissemination across continents. In this work, a multiresidue analytical method suitable for the determination of five families of antibiotics and their main metabolites in waterbird faeces has been developed and validated. The target compounds include environmentally significant sulfonamides, macrolides, fluoroquinolones, tetracyclines and antifolates. Sample treatment involves ultrasound-assisted extraction with methanol and dispersive solid-phase extraction clean-up with C18. Analytical determination was carried out by liquid chromatography–tandem mass spectrometry. The most significant parameters affecting sample extraction and extract clean-up were optimised by means of experimental designs. Good linearity (R2 > 0.994), accuracy (from 41 to 127%), precision (relative standard deviation lower than 24%) and limits of quantification (lower than 2 ng g−1 (dry weight, dw)) were obtained for most of the compounds. The method was applied to the determination of the selected compounds in 27 faeces samples from three common migratory waterbird species. Nine antibiotics and three of their metabolites were detected in the analysed samples. Fluoroquinolones and macrolides were the antibiotics most frequently detected. The highest concentrations corresponded to norfloxacin (up to 199 ng g−1 dw). Graphical abstract