Nitrogen dynamics at ecosystem levels profoundly impact the Earth’s surface system due to their environmental and ecological significance. Exploring the sources and transformation of nitrogen in various Critical Zones is vital to understanding biogeochemical cycles and sustainable development. This study summarized nitrogen characteristics in soil profiles and nitrogen dynamics in diverse terrestrial ecosystems based on data from typical Critical Zones of China. The results indicated that nitrogen accumulates in the deep soils of cropland ecosystems due to intensive fertilizer applications, which potentially harms soil functions and water quality. Therefore, it is necessary and meaningful to take adequate measures to alleviate nitrogen accumulation in deep soils. Additionally, surplus nitrogen transported into groundwater and riverine systems from soil has emerged as an important issue for environmental management. There are serious nitrogen pollution issues in many river water and groundwater areas, which could be addressed by reducing the fast leaching and considerable nitrogen accumulation in the vadose zone. Systematic and long-term observational studies are needed to achieve the ultimate goal of ecological conservation and high-quality development. Therefore, future research should consider monitoring and evaluating ecosystems based on the long-term Critical Zone Observatories networks to advance appropriate environmental management strategies that adapt to nature’s rules and strengthen the ecosystem service function for sustainable development.

About half of the global drinking water comes from groundwater, yet groundwater quality is threatened by high nitrate concentrations globally. Our understanding of groundwater nitrate concentrations is often limited by inaccessibility of groundwater and scarcity of nitrate data in groundwater. Here we used machine learning and decision tree-heatmap analysis by compiling nitrate concentrations and isotope data from 4047 groundwater sites across China to understand their dynamics and drivers across gradients of geographical, climate, and human factors. Results show that nitrate concentrations vary substantially over depth and are generally lower in deeper groundwater, indicating potentially higher nitrate removal rates according to nitrate isotopic pattern such as denitrification at depth. At similar groundwater aquifer depths, nitrate concentrations are highest in urban regions with high population density. In addition, nitrate concentrations are generally higher in arid northern China than humid southern China. Interestingly, while groundwater nitrate concentrations are lower at deeper depths, slow groundwater flow also indicates prolonged nitrogen legacy. Although there has been an overall decline in groundwater nitrogen pollution in China since 2016, persistent pollution has lingered. Future strategies for groundwater quality protection in China should address the long-term legacy of nitrate in different aquifers and rising nitrogen levels in groundwater.