In this study, a comprehensive evaluation model of ammonia pollution trends in a groundwater source area along a river in residential areas is proposed. It consists of coupling models and their interrelated models, including (i) MODFLOW and (ii) MT3DMS. The study area is laid in a plain along a river, where a few workshops operate and groundwater is heavily contaminated by domestic pollutants, agricultural pollutants, and cultivation pollutants. According to the hydrogeological conditions of the study area and the emissions of ammonia calculated in the First National Pollution Source Census Report in China, this study calibrates and verifies the prediction model. The difference between the observed water level and the calculated water level of the model is within the confidence interval of the test. This means that the model is reliable and that it can truly reflect changes in the groundwater flow field and can be directly used to simulate the migration of ammonia. The simulation results show that, after 20 years, the center of the ammonia pollution plume will gradually flow east along with the groundwater over time, mainly affecting the groundwater, which is less than 200 m from the river, and the ammonia content near wells at a maximum extent of less than 0.3 mg/L.