The application of animal manure containing antibiotic residues as an organic fertilizer to farmlands, poses a major threat to the health of river basin ecosystems. Waste treatment processes can help reduce antibiotic pollution levels in river basins following manure application, but the overall influence of these processes remains unclear. This study evaluates the impact of manure treatment methods on the emission and subsequent river pollution caused by 14 frequently detected antibiotics in a typical pig breeding area in China, by using hypothetical scenarios method. Three scenarios were constructed based on possible fate pathways of antibiotics, representing in 47.0, 55.3, and 81.6 ton·yr−1 antibiotic emissions into the river basin. The soil and water assessment tool (SWAT) model successfully simulated the transport of antibiotics from farmland to surface water, with calibration and verification performed using hydrological station monthly data over 8 consecutive years. Field measured concentrations also verified the reliability of the model and were used to determine the most realistic scenario. In basins applied with manure, environmental antibiotic pollution is most affected by the wastewater treatment process and manure applied patterns, followed by changes in streamflow. The antibiotic pollution in manure applied areas showed significant spatial and temporal differences, resulting from the different manure application patterns. The simulated total outflow of antibiotics in the river basin accounted for 18.1% of the inflow, with the loss of target antibiotics by degradation, volatilization and sedimentation deposition in the river basin being 0.23, 0.01 and 33.2 ton·yr−1, respectively. This study can help to clarify the environmental fate of antibiotics in the basin following manure application, provide guidance for policy makers and help to design the effective corrective interventions for reducing the environmental pollution.