A spatially referenced biophysical model, the water and nitrogen management model (WNMM), was developed and shown to simulate dynamic soil water movement and soil–crop carbon (C) and nitrogen (N) cycling under a given agricultural management, for the purpose of identifying optimal strategies for managing water and fertiliser N under intensive cropping systems (mainly wheat–maize) in the North China Plain and other regions in the world. A uniform data structure, ARC GRID ASCII format, was used both in GIS and WNMM for achieving a close Model-GIS coupling. A significant part of WNMM adopts and modifies concepts and components from widely used models, with a focus on soil N transformations. WNMM simulates the key processes of water dynamics in the surface and subsurface of soils: including evapotranspiration, canopy interception, water movement and groundwater fluctuations; heat transfer and solute transport; crop growth; C and N cycling in the soil–crop system; and agricultural management practices (crop rotation, irrigation, fertiliser application, harvest and tillage). The model runs on a daily time step at any desired scale and is driven by lumped variables (meteorological and crop biological data) in text data format, and spatial variables (soil and agricultural management) in ARC GRID ASCII format. In particular, WNMM simulates all key N transformations in agricultural fields, including mineralisation of fresh crop residue N and soil organic N, formation of soil organic N, immobilisation in biomass, nitrification, ammonia (NH3) volatilisation, denitrification and nitrous oxide (N2O) emissions.