A spatially-referenced and process-based biophysical model, the Water and Nitrogen Management Model (WNMM), was developed to simulate soil water movement and soil-plant C and N cycling under given agricultural management practices, for the purpose of identifying optimal strategies for managing water and fertiliser N under intensive wheat-maize cropping systems in the North China Plain. A uniform data structure, ARC GRID ASCII format, is used both in GIS and WNMM for achieving a close Model-GIS coupling. The WNMM simulates the key processes of water, C and N dynamics in the atmosphere-plant-soil system, including evapotranspiration, canopy interception, water movement, groundwater fluctuations, heat transfer, solute transport, crop growth, and agricultural management practices (rotation, irrigation, fertiliser application, harvest and tillage). It runs at a daily time step at different scales, driven by lumped variables (climatic data and crop biological data) in text data format and spatial variables (soil and agricultural management practices) in ARC GRID ASCII format data. In particular, the WNMM simulates all key N transformations in agricultural fields, including mineralisation of fresh plant residue N and soil organic N, formation of soil organic N, dynamics of microbial biomass, nitrification, ammonia volatilisation, denitrification, urea hydrolysis, nitrate leaching and nitrous oxide emissions from soils. Based on WNMM, a user-friendly GIS-based agricultural decision support tool has been developed for optimal irrigation and N fertiliser management for wheat and maize systems in the North China Plain. The tool significantly assisted the adoption of recommended best management practices by farmers and resulted in the annual reductions in fertilizer use around 20-23% while maintaining the crop yield, with the substantial economical benefit.