The occurrence of antibiotics in the marine environment over a long time period can lead to development of antibiotic resistant bacteria, which is a major scientific concern. This study was carried out to investigate the occurrence of four antibiotics (sulfadiazine, sulfamerazine, sulfamethoxazole and trimethoprim) in the waters of Huangpu River and Pearl River Estuary and the East China Sea. To our knowledge, our results are the first findings of antibiotics in the East China Sea. The antibiotics were extracted from water and enriched via solid-phase extraction (Chromabond®EASY). The analysis was carried out with a liquid-chromatography tandem mass spectrometer equipped with a heated electrospray ionization source (HPLC-HESI-MS/MS). The selected antibiotics were detected in all three waters at low ng/L concentrations, which are comparable to literature data. In the Huangpu River the antibiotics occurred at a relatively stable concentration, with a slight decrease towards the Changjiang River. In the East China Sea antibiotics were mainly found in the surface water. Only sulfamethoxazole was found at three stations in bottom water. Detected concentrations in the Pearl River Estuary displayed an inverse correlation with salinity, confirming the dominant effect of dilution due to mixing of riverine and oceanic waters.