The mobility of pharmaceuticals in environmental systems is under great scrutiny in the scientific literature and in the press. Still, very few reports have focused on redox-driven transformations when these compounds are bound to mineral surfaces, and how their transport is affected under flow-through conditions. In this study, we examined the adsorption and electron transfer reactions of ciprofloxacin (CIP) in a dynamic column containing nanosized hematite (α-Fe2O3). CIP binding and the subsequent redox transformation were strongly dependent on inflow pH and residence time. These reactions could be predicted using transport models that account for adsorption and transformation kinetics. Our results show that flow interruption over a 16 h period triggers oxidation of hematite-bound CIP into byproducts. These reactions are likely facilitated by inner-sphere iron-CIP complexes formed via the sluggish conversion from outer-sphere complexes during interrupted flow. When intermittent flow/no-flow conditions were applied sequentially, a second byproduct was detected in the column effluent. This work sheds light on a much overseen aspect of redox transformations of antibiotics under flow-through conditions. It has important implications in adequately predicting transport, and in developing risk assessments of these emerging compounds in the environment.