Diffuse Nitrogen pollution from agriculture maintains high pressures on groundwater and aquatic ecosystems. Further mitigation requires targeted measures that reconcile agricultural interests in environmental protection. However, the agriculture-related processes of catchment N modeling remain poorly defined due to discipline-specific data and knowledge gaps. Using field-experimental data, crop N uptake responses to fertilizer management were parsimoniously conceptualized and integrated into a catchment diffuse-N model. The improved catchment modeling further facilitated integration with agricultural budget-based assessments. The integrated analysis in a mesoscale catchment disentangled contrasting agri-environment functional mechanisms in typically flashy chemodynamic and transport-limited chemostatic export regimes. Moreover, the former was actively responsive to interannual climatic variability and agricultural practices; the latter exhibited drought-induced enhancement of N enrichment, which could likely be mitigated through reduced fertilization. This interdisciplinary integration of data and methods provided an insightful evidence base for multi-sector targeted measures, especially under cumulative impacts of changing climate and fertilizer-use intensities.