Rice–wheat cropping systems occupy between 24 and 26 Mha in Asia. A main feature of RW rotations is the alternation of aerobic and anaerobic soil conditions. This alternation of flooded and non-flooded soil conditions is conducive to N emissions, especially with the current high N rates in RW systems. To design alternative management systems, better understanding of the processes underlying emissions is required. For that purpose, the RIce WhEat Rotation model (RIWER) was developed, on the basis of existing crop, water and soil organic matter models, describing the relevant soil processes under both anaerobic and aerobic conditions. RIWER is evaluated using data from RW experiments in China. Assessment of model performance, on the basis of graphical comparison and goodness-of-fit parameters, showed that RIWER performs well in simulating total aboveground biomass, N uptake of cops and soil inorganic N content. The RIWER modeling framework needs further testing, but offers a promising operational tool to support the design of sustainable RW systems, combining environmentally-friendly production methods and high yields.