Many pumping and treating systems tend to consider more about the efficiency of earlier remediation period, and this causes the low efficiency and the towing tail phenomenon at the end of remediation period. Efficiently capturing the flow of contaminated groundwater is the key technology in the pumping and treating remediation system optimization. Solute transport simulation can offer guidance for the design of pumping wells and schemes. Many previous studies focused on the coupling of the model and optimization algorithm, such as the Modular Groundwater Optimizer (MGO), but MGO can only apply to a steady flow model. In this study we choose to conduct a lot of artificial trial calculation by GMS instead of MGO because the transient flow model is more realistic than the steady flow. In addition, we verify the model not only by groundwater level data, but also by solute concentration data at 4 times to make sure the more accurate model. This study is aim to optimize the pumping and treating system, and reduce the period and the cost for the remediation of ammonia contaminated groundwater in a chemical fertilizer plant site in northern China. Based on the hydrogeological survey and ammonia nitrogen concentration monitoring, we arrange the pumping wells in the central axis and on both sides of the contamination plume combining the central axis method and the triangle method. After a lot of trial calculation by GMS, three pumping -and -treating schemes are simulated and evaluated, considering the number of wells, remediation period and the whole volume of sewage. Finally, scheme 3 is thought to be the most optimal scheme. Its remediation period is 1 year and 11 months shorter than that of scheme 1, and its sewage volume is 319 million liter less than that of scheme 1. The simulation results show that reasonable arrangement of wells and pumping mode by stages is the key factor to make sure the contaminant plume to be remediated completely and efficiently. Besides, in a groundwater remediation project, the contaminant concentration in groundwater should be monitored regularly and the simulation should be adjusted accordingly. The remediation scheme can be revised in time to ensure that the high concentration zone always has pumping wells with large flow rate.