The occurrence of 22 antibiotics in water samples, sediments, fish and shellfish in aquaculture area of the Pearl River Estuary (Zhuhai and Daya Bay) was studied, using ultrasonic extraction combined with ultraperformance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). The main pollutants detected in aquaculture area of the Pearl River Estuary are quinolones such as norfloxacin, ofloxacin, ciprofloxacin and flumequine. Higher Σantibiotics were observed in Zhuhai Bay in water and sediments compared with Daya Bay. The concentrations of antibiotics in water samples, ranging from 0.13 (sulfamethoxazole) to 4.68 (spectinomycin) ng/L on average, were strongly affected by precipitation. The concentrations of antibiotics in sediments, ranging from 0.02 (isochlortetracycline) to 8.77 (spectinomycin) ng/g (dry weight) on average, accumulated over time. The concentrations of antibiotics in seafood ranged from 0.06 (sulfamerazine) to 46.75 (norfloxacin) ng/g (dry weight). The concentration levels of antibiotics in shellfish and fish were similar and did not show any significant difference. The correlation analysis showed that the concentration levels of antibiotics among sediments were the same; for most seafood, it was same; and for water samples, the difference was great.