This article discusses the generation and migration process of nitrate-N pollution in shallow groundwater caused by agricultural nonpoint source pollution in the catchment area of Shitoukoumen Reservoir in northeast China. By monitoring the shallow groundwater nitrate-N in the low-water period, the normal season, and high-flow period in the study area for a year, it was found that the nitrate-N concentration in the shallow groundwater of this area had a seasonal variation in both spatial and time distribution. In the time distribution, the peak value appeared in July, the high-flow period, and the valley value appeared in April, the low-water period, and showed a significant correlation with the time distribution of fertilization rate and rainfall. In the spatial distribution of nitrate-N pollution, when the distribution in shallow groundwater was analyzed separately in the three different periods (low-water period, the normal season, and high-flow period) and the discipline transference and enrichment of nitrate-N pollution in shallow groundwater was determined, this indicated that the region in the southeast study area where runoff conditions were better was less contaminated, and the region where runoff conditions were poor, as well as the region along the river were seriously polluted. The nitrate-N concentration in shallow groundwater was distributed mainly along the path of groundwater flow and was excreted in the drainage region. This showed that the spatial distribution of nitrate-N concentration in the shallow groundwater of the entire region was mainly controlled by the groundwater flow system. At the same time, in the middle and lower reaches of the study area, the seasonal changes in the recharged-excreted relationship between groundwater and river caused seasonal differences in the spatial distribution of nitrate-N pollution in groundwater. The combined effects of the groundwater mobility and the surface river resulted in a poor correlation between the groundwater nitrate-N concentration and land-use types. Only in the plain area where there was little influence from groundwater runoff and the surface river did the groundwater nitrate-N concentration correlate with land-use types. The spatial and time distribution of nitrate-N concentration in the shallow groundwater of the study area was impacted by agricultural nonpoint source pollution, the groundwater flow system, and the surface river and formed a concentration response system which uses basins as a unit.