A drinking-groundwater source protection technology system based on a three-dimensional finite-difference groundwater model was constructed and applied to the safe management of drinking groundwater in the first terrace of Fujiang River. In the study area, the main type of groundwater is the quaternary systemic alluvial deposit loose rock pore water and the aquifer thickness varies between 20 and 35 m. Groundwater is the main source of water and is used for various purposes through two exploitation wells. The water volumes of 1# exploitation well (1#) and 2# exploitation well (2#) are 10,000 m3/day and 5000 m3/day, respectively. An analysis of 22 indicators from 11 groundwater samples showed that a higher concentration of chemical-oxygen-demand (CODMn) and ammonia-nitrogen (NH3-N), and they had a high correlation with most of the other water-quality factors. Therefore, CODMn and NH3-N were selected as indicator factors for model calibration and prediction. Twenty-two hydraulic head observation wells were used for flow-model calibration. The flow model indicated that a drop funnel formed with a maximum depth of 12 m, and the particle-capture zone in the original downstream direction of the south side extended to 1100 m because of groundwater exploitation. The solute-transport model showed that industrial pollution sources were the main factors that led to a deterioration of water quality. To analyze the necessity and effectiveness of remediation measures for the safety of drinking-water sources, two scenarios were considered to predict the concentration of NH3-N and CODMn in groundwater exploitation wells over 20 years. Scenario I, which considered that current conditions were maintained, predicted that the NH3-N would exceed the drinking-water quality standard of 0.5 mg/L after 16 years. Scenario II, in which industrial sewage treatment plants were installed outside the particle-trapped zone of the exploitation wells and strict anti-seepage measures were implemented, predicted that the peak concentrations of NH3-N and CODMn in the exploitation wells would be 0.26 mg/L and 1.33 mg/L, respectively, after 3 years of model operation. This study provides a theoretical basis for drinking-groundwater source protection that can be applied to safety management practices.