Residue levels of the antibacterials enrofloxacin and ciprofloxacin were analysed in 15 commercially relevant animal by-products (ABPs). Enrofloxacin was detected in all ABPs, and ciprofloxacin was detected in 11 of 15 ABP samples. Feed to muscle and skin carry –over of low background enro- and ciprofloxacin levels were assessed by applying a simple toxicokinetic model. The muscle and skin uptake and elimination rates were established in Atlantic salmon (Salmo salar L.) fed enrofloxacin enriched diets (100 μg kg−1 ‘low’ and 4000 μg kg−1 ‘high’) in triplicate for 41 days followed by a 90 days depuration period. The terminal half-lives were 17 ± 0.4 and 18 ± 0.7 days, and uptake rates were 9.3 ± 3.3 and 11 ± 3.1 (day−1) for the ‘low’ and ‘high’ groups, respectively. Only fish fed high background levels had quantifiable levels of the metabolite ciprofloxacin with a formation of 0.25 ± 0.01% day−1. The toxicokinetic carry-over model predicted muscle and skin steady state levels of 1.8 μg kg−1 when fed theoretically high enrofloxacin levels (158 μg kg−1), which is below the EU limit of 100 μg kg−1 for enrofloxacin in finfish food products. The antibacterial residue levels could however be detected in EU food surveillance programmes.