The pollution of antibiotics commonly existed throughout the entire aquaculture process, but the residues of antibiotics at different aquaculture stages have rarely been studied. This study investigated the occurrence, distribution and risk assessment of antibiotics at different aquaculture stages (the non-aquaculture stage, the early aquaculture stage, the middle aquaculture stage, and the late aquaculture stage) in two typical marine aquaculture areas (Mahegang River and Dingzi Bay) surrounding the Yellow Sea. Fluoroquinolones and tetracyclines were commonly used antibiotics in the aquaculture of these areas with high detection frequencies (17% to 83%). Compared among four aquaculture stages, the highest concentration of antibiotics (9032.08 ng/L) in aquaculture ponds was detected at the late aquaculture stage. And the antibiotic pollution level of natural water was directly related to the aquaculture stages. Similarly, at the aquaculture stages, the detection frequency of antibiotics in sediments was higher than that at the non-aquaculture stage. Based on the correlation analysis, the concentration of main antibiotics in water showed a positive correlation with total nitrogen (p<0.05) and chlorophyll a (p<0.01), while it showed a negative correlation with salinity (p<0.01) in coastal water of the Dingzi Bay. According to the risk assessment, with the development of aquaculture stages, the selection pressure of fluoroquinolones and tetracyclines on resistant bacteria had increased. And the ecological risks caused by sulfonamides and tetracyclines to aquatic organisms had also increased markedly. Overall, this study may provide a reference for formulating regulatory policies regarding antibiotic use at different aquaculture stages.