Groundwater recharge from rainstorms can be vital for regional water resources. With the expansion of the need for more water in some specific regions under global climate change, groundwater is being pumped at a far greater rate than it can be naturally replenished. Considering that excess rainstorms could be utilized for groundwater recharge to lessen the declining tendency of regional groundwater level in the Sanjiang Plain, Northeast China, we analyzed groundwater changes in the quantity of a regional shallow aquifer in the region following extreme rainfall in 2013. The results show that shallow groundwater table in the north and central Sanjiang Plain increased following the 2013 extreme rainfall. Most of the annual maximal change of groundwater depth (MCGD) was in the range of 1 m to 3 m, occupying 72.1% of the study area. The average MCGD was 1.73 m in 2013, about 0.4 m higher than the mean value during the last five years (1.33 m). Spatially, the overall average groundwater depth showed an increasing trend from the southeast to the midwest and northeast. We estimated a total recharge of approximately 41.14 × 108 m3 from the 2013 extreme rainfall across the north and central Sanjiang Plain. This large quantity of recharge demonstrates the important role that large rainstorms can play in regional shallow groundwater resources.