A sensitive liquid–chromatography–electrospray tandem mass spectrometry multiclass method for determination of 45 veterinary compounds belonging to 9 different antibiotic groups, including aminoglicosides (4), β-lactams (13), diaminopyrimidines (1), fluoroquinolones (10), lincosamides (1), macrolides (5), pleuromutilins (1), sulfonamides (6) and tetracyclines (4), in water from breeding animal watering supply system has been developed. Isolation of the analytes was carried out by solid phase extraction with heptafluorobutyric acid as an ion-pair agent on the Strata-X reversed phase cartridges. All analytes were determined simultaneously in one single run on a C18 column with gradient elution and short analysis time (13min). Method was validated, average relative recoveries were in the range of 84.3–109.3% with satisfactory precision are repeatability for all compounds are in the range of 4.7–12.2%, within-laboratory reproducibility are in the range of 4.4–13.5% for. The limit of quantitation (LOQ) of the method was in the range of 0.02–10μgL−1, depending of analyte. The applicability of the method was tested by determining antimicrobial compounds in real water samples collected from water supply systems in breeding animal farms. The average antibiotics concentration in real water samples were, respectively, in the range of 0.14–1670μgL−1.