Water N-NO3− (mg L−1) pollution is attracting global concern in the face of combating climate change and human health risks. However, there have been comparatively few comprehensively researched studies on water N-NO3− pollution with respect to N-NO3− deposition, soil nitrogen, and land-use changes. We collected a total of 7707 published sampling points on N-NO3− surface and groundwater during flooding and non-flooding seasons during 2000–2020 in China. The types of water N-NO3− pollution (>20) can be categorized as point pollution (ΔTN ≤ 0 or > 1.5) and non-point pollution (0 < ΔTN ≤ 1.5), which were then assessed with respect to soil nitrogen (ΔTN g kg−1) and water N-NO3− changes in this study. We found non-point pollution was concentrated in the Huaihe River Basin and Haihe River Basin with higher urbanization (+6%, +4%), cropland (72%, 45%), nitrogen fertilization (g m−2 yr−1) (>10), and increased wet N-NO3− deposition (WND) (kg ha−1 yr−1) (+4.6, +3). The Haihe River Basin was found to have the highest N-NO3− on its surface (306) and in its groundwater (868) and nitrogen fertilization (32). Point pollution was concentrated in the Songhua and Liaohe River Basin with the highest WND (+7.9) but slow urbanization (+1%). N-NO3− increased during the flooding season compared with the no-flooding season in serious pollution areas. N-NO3− increased in the Liaohe River and middle and low Yangtze River but was reduced in the Weihe River. Therefore, stringent criteria and management, especially during the flooding season are urgently required to mitigate the degree of N-NO3− water pollution that occurs due to intensive agriculture and urbanization with increased N-NO3− deposition.