Increasing diffuse nitrate loading of surface waters and groundwater has emerged as a major problem in many agricultural areas of the world, resulting in contamination of drinking water resources in aquifers as well as eutrophication of freshwaters and coastal marine ecosystems. Although empirical correlations between application rates of N fertilizers to agricultural soils and nitrate contamination of adjacent hydrological systems have been demonstrated, the transit times of fertilizer N in the pedosphere–hydrosphere system are poorly understood. We investigated the fate of isotopically labeled nitrogen fertilizers in a three–decade-long in situ tracer experiment that quantified not only fertilizer N uptake by plants and retention in soils, but also determined to which extent and over which time periods fertilizer N stored in soil organic matter is rereleased for either uptake in crops or export into the hydrosphere. We found that 61–65% of the applied fertilizers N were taken up by plants, whereas 12–15% of the labeled fertilizer N were still residing in the soil organic matter more than a quarter century after tracer application. Between 8–12% of the applied fertilizer had leaked toward the hydrosphere during the 30-y observation period. We predict that additional exports of ¹⁵N-labeled nitrate from the tracer application in 1982 toward the hydrosphere will continue for at least another five decades. Therefore, attempts to reduce agricultural nitrate contamination of aquatic systems must consider the long-term legacy of past applications of synthetic fertilizers in agricultural systems and the nitrogen retention capacity of agricultural soils. Significance Fertilizers are of key importance to sustain modern agriculture, but the long-term fate of fertilizer-derived nitrogen in the plant–soil–water system is not fully understood. This long-term tracer study revealed that three decades after application of isotopically labeled fertilizer N to agricultural soils in 1982, 12–15% of the fertilizer-derived N was still residing in the soil organic matter, while 8–12% of the fertilizer N had already leaked toward the groundwater. Part of the remaining fertilizer N still residing in the soil is predicted to continue to be taken up by crops and to leak toward the groundwater in the form of nitrate for at least another five decades, much longer than previously thought.

Denitrification is the main process removing nitrate in river drainage basins and buffer input from agricultural land and limits aquatic ecosystem pollution. However, the identification of denitrification hotspots (for example, riparian zones), their role in a landscape context and the evolution of their overall removal capacity at the drainage basin scale are still challenging. The main approaches used (that is, mass balance method, denitrification proxies, and potential wetted areas) suffer from methodological drawbacks. We review these approaches and the key frameworks that have been proposed to date to formalize the understanding of the mechanisms driving denitrification: (i) Diffusion versus advection pathways of nitrate transfer, (ii) the biogeochemical hotspot, and (iii) the Damköhler ratio. Based on these frameworks, we propose to use high-resolution mapping of catchment topography and landscape pattern to define both potential denitrification sites and the dynamic hydrologic modeling at a similar spatial scale (<10 km²). It would allow the quantification of cumulative denitrification activity at the small catchment scale, using spatially distributed Damköhler and Peclet numbers and biogeochemical proxies. Integration of existing frameworks with new tools and methods offers the potential for significant breakthroughs in the quantification and modeling of denitrification in small drainage basins. This can provide a basis for improved protection and restoration of surface water and groundwater quality.