Designing sustainable rice-based production systems through waterlogging-adapted winter crop diversification

Context Rice-based double-cropping systems are increasingly challenged by seasonal waterlogging and climate change, yet the long-term implications of winter crop selection for whole-system performance remain poorly understood. Objective To quantify the relative importance of winter crop selection and future climate change in determining the productivity, resource-use efficiency and resilience of rice-based cropping systems. Methods An improved APSIM framework was developed and evaluated using multi-year field observations from four rice-based crop rotations. The validated model was applied under historical climate and three 2050s climate scenarios, and system performance was assessed using agronomic, economic and environmental indicators. Results and conclusions Interannual climate variability had the greatest influence on system yield in the 2050s, explaining 65.6% of total variance, while crop type explained 37.3% of cumulative waterlogging-stress variance. Rice–wheat was consistently the most vulnerable rotation, with waterlogging-induced yield penalties increasing from 5.9% under the historical climate to 9.8% under SSP585. Rice–faba bean showed the most balanced multidimensional performance, combining strong waterlogging resilience, high simulated profitability, high fertiliser-based nitrogen use efficiency and low greenhouse gas intensity. Waterlogging also increased nitrogen losses and N 2 O emissions while reducing nitrogen use efficiency, particularly in the rice–wheat and rice–canola rotations. Significance This study shows that crop selection and climate variability influence different dimensions of rice-based system performance. Although annual productivity was strongly affected by interannual climate variability, winter crop selection substantially influenced seasonal waterlogging stress and the comparative performance of alternative rotations. The findings support crop diversification as an adaptation strategy for regions facing increasing waterlogging risk.