Contamination of trace antibiotics is widely found in surface water sources. This work delineates removal of trace antibiotics (norfioxacin (NOR), sulfadiazine (SDZ) or tylosin (TYL)) from synthetic surface water by flocculation, in the coexistence of inorganic suspended particles (kaolin) and natural organic matter (humic acid, HA). To avoid extra pollution caused by petrochemical products-based modification reagents, environmental-friendly amino-acid-modified-chitosan flocculants, Ctrp and Ctyr, with different functional aromatic-rings structures were employed. Jar tests at various pHs exhibited that, Ctyr, owning phenol groups as electron donors, was favored for elimination of cationic NOR (similar to 50% removal; optimal pH: 6; optimal dosage: 4 mg/L) and TYL (similar to 60% removal; optimal pH: 7; optimal dosage: 7.5 mg/L), due to pi-pi electron donator-acceptor (EDA) effect and unconventional H-bonds. Differently, Ctrp with indole groups as electron acceptor had better removal rate (similar to 50%) of SDZ anions (electron donator). According to correlation analysis, the coexisted kaolin and HA played positive roles in antibiotics' removal. Detailed pairwise interactions in molecular level among different components were clarified by spectral analysis and theoretical calculations (density functional theory), which are important for both the structural design of new flocculants aiming at targeted contaminants and understanding the environmental behaviors of antibiotics in water. (C) 2016 Elsevier B.V. All rights reserved.