To keep groundwater levels stable, Jinan’s government has implemented several water management measures. However, considerable volumes of dissolved organic carbon (DOC) can enter groundwater via water exchange, impacting groundwater stability. In this study, a SWAT-MODFLOW-RT3D model designed specifically for the Yufu River Basin is developed, and part of the code of the RT3D module is modified to simulate changes in DOC concentrations in groundwater under different artificial recharge scenarios. The ultimate objective is to offer valuable insights into the effective management of water resources in the designated study region. The modified SWAT-MODFLOW-RT3D model simulates the variations of DOC concentration in groundwater under three artificial recharge scenarios, which are (a) recharged by Yellow River water; (b) recharged by Yangtze River water; and (c) recharged by Yangtze River and Yellow River water. The study shows that the main source of groundwater DOC in the basin is exogenous water. The distribution of DOC concentration in groundwater in the basin shows obvious spatial variations due to the influence of infiltration of surface water. The area near the upstream riverbank is the earliest to be affected. With the prolongation of the artificial recharge period, the DOC concentration in groundwater gradually rises from upstream to downstream, and from both sides of the riverbank to the surrounding area. By 2030, the maximum level of DOC in the basin will exceed 6.20 mg/l. The Yellow River water recharge scenario provides more groundwater recharge and less DOC input than the other two scenarios. The findings of this study indicate that particularly when recharge water supplies are enhanced with organic carbon, DOC concentrations in groundwater may alter dramatically during artificial recharge. This coupled modeling analysis is critical for assessing the impact of recharge water on groundwater quality to guide subsequent recharge programs.