The fractionation of natural organic matter (NOM) and its impact on the binding of quinolones to mineral surfaces and transport behavior under flow-through conditions have been scarcely investigated. In this study, the sorption and transport of a widely used quinolone antibiotic, Nalidixic acid (NA), were investigated in goethite-coated sand (GCS) columns over a wide concentration range (5-50 mg/L) of Leonardite humic acid (LHA), a representative NOM. Simultaneous injection of NA and LHA in GCS columns mutually alter transport of each other, i.e. NA mobility and LHA molecular fractionation. Preloading of GCS column with LHA dramatically facilitated the transport behavior of NA, where nonspecific interactions with LHA-covered goethite surfaces controlled NA mobility. Simulations using a two-site nonequilibrium model showed that a modified sorption rate constant was required to accurately describe the breakthrough curves of NA under these conditions. This altered rate constant suggests that nonspecific interactions of NA on bound LHA may take place as an additional binding mechanism affecting adsorption kinetics. NOM fractionation alters sorption mechanisms and kinetics of quinolone antibiotics, which in turn affect their fractionation. These results may have important implications for an accurate assessment of the fate of these types of antibiotics in aquatic environments.