Abstract: Nitrate leaching from Chinese farmland causes non-point source pollution and is an increasingly serious issue. The vadose zone is an important place for nitrate nitrogen accumulation and storage and a common way for nitrate to leach into the groundwater. Nitrate spatial-temporal changes in the underground water and vadose zones were analyzed in this study. Farmlands in black soil, fluvo-aquic soil, and cinnamon soil in northern China were investigated by monitoring underground water nitrate and water level changes to determine the underground water nitrate contents. The results showed that the black soil region (Northeast China) had the highest groundwater nitrate content with excess standard rate of 39.6%, followed by the fluvo-aquic soil region (North China) (19.3%); the cinnamon soil region (Northwest China) had the lowest rate (14.9%). In the North China Plain, the excess standard rates of nitrate in shallow underground water trended upward over the years; the groundwater nitrate excess standard rate was 11.8% in 1998 and 18.9% from 2016 to 2018. The underground water nitrate excess standard rate was higher in vegetable-planting areas than in grain crop-planting areas. Soil nitrate was distributed and accumulated in the vadose zone before being leached into the underground water. Nitrate accumulation increased with vadose zone thickness; the total nitrate-N storage in the North China Plain deep vadose zone was up to 18.54 million tons. Nitrate accumulated mainly at a depth of 0–6 m, and crop production contributed, on average, 78.3% toward the regional vadose zone nitrate storage.