Urbanization and climate change exacerbate groundwater overexploitation and urban flooding. The infiltration basin plays a significant role in protecting groundwater resources because it is a prevalent technology of managed aquifer recharge. It could also be utilized as a retention pond to mitigate city waterlogging. The goal of this study was to explore the offsets of artificial recharge on the extra runoff induced by urbanization and extreme storms via infiltration basins. To achieve this objective, a lumped infiltration basin module was developed and integrated into a semi-distributed hydrologic model. Then, the enhanced model was applied to an agriculture watershed with urban areas. Finally, the functionalities of the infiltration basins were evaluated under the scenarios of the predicted urbanization and extreme storms. The results demonstrated the capability of the infiltration basins to influence both artificial recharge and flood mitigation. To mitigate floods, especially peak flows, larger areas are needed for infiltration basins than for artificial recharge purposes only. Based on different demands, the intermittent regulation of infiltration basins according to different hydrologic periods is recommended. The offsets of artificial recharge on the extra surface runoff provide insight into the comprehensive preservation and management of surface water resources and groundwater resources.