The SWAT model primarily investigates sources of water pollution and conducts ecological assessments of surface water in contemporary hydrology and water resources research. To date, there have been limited accomplishments in the study of groundwater resources in China. The MODFLOW model currently primarily simulates groundwater levels and the migration of water quality, depending on the hydrological surface water data in the relevant area. This study aims to investigate the groundwater distribution characteristics of the middle and lower reaches of the Songhua River, a significant agricultural and grain production region in China. The research focuses on the middle and lower reaches of the Songhua River basin in Northeast China and employed the SWAT distributed hydrological model to simulate runoff. The monthly recorded runoff at Tongjiang Station in Jiamusi City was utilized to calibrate the model parameters. Consequently, the MODFLOW model was introduced to compare and assess the simulation outcomes of the SWAT model, ultimately ascertaining the distribution characteristics of shallow groundwater, groundwater recharge, recoverable volume, and groundwater levels in the Songhua River Basin. The findings indicate that: (1) The SWAT model demonstrates efficacy in the study region, achieving R2 and NS values of 0.81 and 0.76, respectively, thereby fulfilling the fundamental criteria for scientific research. The MODFLOW model exhibits strong performance in the study region, achieving a periodic R2 of 0.98 and a verification R2 of 0.97, with the discrepancy between simulated and actual groundwater levels confined to 0.6 m, thereby satisfying the criteria for scientific research. (2) In 2011, 2014, and 2016, the groundwater recharge in the middle and lower sections of the Songhua River was 24.33 × 108 m3, 30.79 × 108 m3, and 32.25 × 108 m3, respectively, aligning closely with the SWAT simulation results, while the average annual groundwater level depth was 8.17 m. (3) In the research area, groundwater recharging occurs primarily by atmospheric precipitation, while drainage predominantly transpires via groundwater as base flow, constituting 81.46%. Secondly, the recharge of shallow groundwater to deep aquifers is around 7.14%, with a minimal share attributed to vadose zone loss, constituting merely 2.1%. (4) From 2010 to 2016, the average groundwater runoff modulus of the middle and lower reaches of the Songhua River basin was 1.005 L/(s·km²), with a total recharge of 216.58 × 108 m3 and a total recoverable amount of 105.11 × 108 m3. The mean yearly supply was 25.11 × 108 m3. The total groundwater recharge was 26.54 × 108 m3 in the driest year (2011) and 33.25 × 108 m3 in the year of most ample water (2016).
