The behavior and removal of six antibiotics, that is, azithromycin, clarithromycin, sulfathiazole, sulfamethoxazole, ciprofloxacin, and tetracycline, in an artificial‐controllable urban river (ACUR) were investigated. The ACUR was constructed to form five artificial eco‐systems by planting three emergent hydrophytes and Microcystis aeruginosa: (1) Control; (2) MA: M. aeruginosa only; (3) MA‐J‐C: M. aeruginosa combined with Juncus effusus and Cyperus alternifolius; (4) MA‐C‐A: M. aeruginosa combined with C. alternifolius and Acorus calamus L.; (5) MA‐A‐J: M. aeruginosa combined with A. calamus L. and J. effusus. The MA‐C‐A system achieved the best removal of azithromycin and clarithromycin after 15‐day test with the final concentrations 0.92 and 0.83 μg/L. The contents of ciprofloxacin and tetracycline in sediment were highest, up to 1453 and 1745 ng/g. The antibiotic plant bioaccumulation was higher in roots rather than the shoots (stem and leaves). No target antibiotics were detected in algae cells. The combination of hybrid hydrophytes had a certain effect on the removal of antibiotics, and thus selecting appropriate hydrophytes in urban rivers could greatly improve water quality. The overall removal of six antibiotics was greatly improved by the ACUR containing the hybrid hydrophytes and the algae, indicating a synergistic effect on antibiotic removal. Practitioner points Controllable‐mobile artificial eco‐systems were developed with emergent hydrophytes and M. aeruginosa. The M. aeruginosa + Cyperus alternifolius + Acorus calamus L. system removed azithromycin and clarithromycin most at the end of tests. Emergent hydrophytes and M. aeruginosa have a synergistic effect on the removal of antibiotics. The combination of emergent hydrophytes did play an important role in the removal of antibiotics. The artificial eco‐systems containing the hybrid hydrophytes and the algae could greatly improve the overall removal of antibiotics.

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