Cation-pi attraction is a major force that determines macromolecular structures and drug-receptor interactions. However, the role of the cation-pi interaction in sorption of fluoroquinolone antibiotics by pyrogenic carbonaceous materials (PCMs) has not been addressed. We studied sorption of ciprofloxacin (CIP) on graphite to quantify the contribution of the cation-pi interaction. Through competition experiments, the decreased amount of sorbed CIP by sequential treatment with hexadecane, phenanthrene and benzylamine represents the contribution of hydrophobic, pi-pi and cation-pi interactions, respectively. Benzylamine competed more strongly with CIP than n-hexadecane and phenanthrene, indicating that cation-pi is a major force. Cation-pi interactions accounted for up to 72.6% of the total sorption at an initial CIP concentration of 0.000015 mmol/L. Importantly, species transformation (CIP(0) captures H+ from water to form CIP(+1)) induced by cation-pi interactions was verified both experimentally and theoretically and can be used to explain the environmental behavior of other fluoroquinolone antibiotics and biochemical processes of amino acids that interact with aromatic moieties. Because of the significant role of cation-pi interactions, CIP desorption increased up to 2.32 times when Na+ increased from 0.01 mM to 0.45 mM, which is an environmentally relevant scenario at river estuaries. Hence, behaviors of fluoroquinolone antibiotics that are affected by ionic strength changes need to be carefully evaluated, especially in river estuaries.