Abstract: After the reform and opening in 1978, China’s nitrogen (N) fertilizer input increased sharply, increasing grain yield, but also causing serious soil nitrate accumulation and leaching problems that threaten groundwater security. This study aimed to explore the effects of N fertilizer input on nitrate storage in the vadose zone of farmlands (grain and vegetable fields) in the North China Plain (NCP) and to quantify the total amount of nitrate leaching from the 2–50 m underground aquifer of the NCP. We collected soil profiles from areas with different groundwater table depths (2–50 m) of the NCP farmlands and measured the nitrate content in different soil layers. Concurrently, data on N fertilizer input and changes in the farmlands of different provinces and counties of the NCP were collected from literatures and relevant websites for 42 years (1978–2019). Nitrate storage in the vadose zone was calculated using a geographic information system (GIS). The ratio of nitrate storage to nitrogen fertilizer input (NR) in the vadose zone was proposed from the perspective of regional blocks. The NR value of grain and vegetable fields in the NCP ranged from 0.14 to 0.39 and from 0.15 to 0.41, respectively. This provided scientific data and a theoretical basis for reducing the leaching loss of nitrate from the vadose zone to the aquifer. The relationship (NR value) between N fertilizer input and nitrate storage in the vadose zone at different groundwater table depths reflects the degree of influence of N fertilization on the amount of residual nitrate in the vadose zone. Moreover, under the same N fertilizer conditions, the leaching loss of nitrate from the NCP farmlands was estimated at groundwater table depths of 2–50 m. The results showed that high fertilizer application in the NCP farmlands led to large amounts of nitrate leaching into the vadose zone-aquifer system. The total nitrate leaching from grain and vegetable fields under 2 m of groundwater was 6.7565 and 1.9956 million tons, respectively, accounting for 13% and 14% of the total N fertilizer input from grain and vegetable fields in 42 years (1978–2019). Under ideal conditions (depth of vadose zone >10 m, the same farmland area and soil texture), higher N fertilizer input was associated with greater total nitrate storage in the vadose zone. Nitrate storage per unit area of farmland (grain and vegetable fields) in the NCP increased with increasing depth of the vadose zone at areas with 2–50 m of groundwater depth. This study also indicated that a thick vadose zone played an important role in nitrate nitrogen interception. In the 2, 3, 6, 10, 16, 25, 40, and 50 m vadose zones, grain field nitrate storage accounted for 14%, 18%, 26%, 30%, 33%, 35%, 38%, and 39% of the total N fertilizer input over 42 years (1978–2019), respectively. Vegetable field nitrate storage at the same depths of the vadose zone accounted for 15%, 20%, 28%, 32%, 34%, 36%, 40%, and 41% of the total N fertilizer input over 42 years (1978–2019), respectively. This study suggests that the relevant departments and agricultural workers should consider the depth of the vadose zone to comprehensively evaluate nitrate nitrogen accumulation and groundwater safety issues from a regional perspective.