Antimicrobial residues may pose harmful effects on the health of consumers. At the sametime, an adequate quality of drinking water for animals is one of the important element to ensureanimal welfare and food without antibacterials. The presented study is aimed at estimating theresidue levels of antibacterial compounds, such as penicillins, cephalosporin, macrolides, tetracy-clines, quinolones, sulphonamides, aminoglycosides, diaminopirymidines, pleuromutilines andlincosamides in meat and on-farm drinking water samples using liquid chromatography-tandemmass spectrometry (LC-MS/MS), as a part of a surveillance system on pig and broiler farms within theproject Healthy Livestock. A total of 870 samples of muscle from pig and broiler, as well as 229 watersamples were analysed for antibiotic residues. Samples were collected from farms in EU countriesin two steps, before and after implementation of a tailor-made health plan. In muscle samples, thedetected concentrations of doxycycline in the post-intervention step (15.9–70.8 μg/kg) were lowerthan concentrations in the pre-intervention step (20.6–100 μg/kg). In water samples, doxycycline inan average concentration of 119 μg/L in the pre- and 23.1 μg/L in the post-intervention step, as wellas enrofloxacin at concentrations of 170 μg/L in the pre- and 1.72 μg/L in the post-intervention stepwere quantified. Amoxicillin was only present before intervention. The obtained results confirm theeffectiveness of the intervention actions. The concentrations of antibiotics in muscles and water werelower after implementation of a health plan on the farms.