Pharmaceuticals used in livestock production may be present in manure and slurry as the parent compound and/or metabolites. The environment may therefore be exposed to these substances due to the application of organic fertilisers to agricultural land or deposition by grazing livestock. For other groups of substances that are applied to land (e.g. pesticides), preferential flow in clay soils has been identified as an extremely important mechanism by which surface water pollution can occur. This lysimeter study was therefore performed to investigate the fate of three antibiotics from the sulphonamide, tetracycline and macrolide groups in a clay soil. Only sulphachloropyridazine was detected in leachate and soil analysis at the end of the experiment showed that almost no antibiotic residues remained. These data were analysed alongside field data for the same compounds to show that soil tillage which breaks the connectivity of macropores formed over the summer months, prior to slurry application, significantly reduces chemical mobility.