In recent years, intense human activities have threatened to dry up the well-known karst springs in Jinan, China. Sponge city construction program was one of the measures aiming to improve the recharge to groundwater and also protect sources of spring discharge. Influence study of sponge city construction on groundwater is necessary while not fully evaluated. In this paper, a three-dimensional numerical groundwater flow model was developed to address this issue. Model calibration showed that the simulated groundwater level successfully reproduced the observed results. Then, 12 scenarios were established and predicted according to different precipitation conditions and the achieved degrees of sponge city construction. The results indicated that the sponge city construction was conducive to the rise of regional groundwater level after 20 years. However, the groundwater level around the spring groups would only increase by an average of 0.22 m, and the annual spring discharge would increase by approximately 9.00 million m3 after 20 years. Results revealed that the extent of spring discharge recovery was not evident in a short time frame. The proper positioning of sponge city construction was suggested to be considered further to balance the protection of springs with the issue of waterlogging.