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The residual of antibiotics in aquatic environment would be difficult to be removed, and cause antibiotic resistance, allergic reactions, or toxic effects to aquatic organisms. The fluoroquinolones (FQs) and sulfonamides (SAs) are two typical kinds of antibiotics, which occupied a high proportion and had been widely used owing to their wide antimicrobial spectra. Ciprofloxacin (CIP) is one of the FQs. When FQs and SAs were released into the environment, these antibiotics could accumulate in soils or sediment and finally transfer to water due to the unbalanced concentrations. The rapid and sensitive analytical methods employed to assess FQs and SAs for aqueous samples are still waiting for the further development. Capillary electrophoresis (CE) is a good alternative tool of HPLC and is regarded as a green analytical technique due to its high separation efficiency, short analysis time and low solvent consumption.