Extreme weather events threaten food security, yet global assessments of impacts caused by crop waterlogging are rare. This study develops a paradigm distilling common stress patterns across environments, genotypes, and climate horizons; embeds improved process-based understanding into a farming systems model to discern changes in global crop waterlogging under future climates; and develops avenues for adapting cropping systems to waterlogging. Yield penalties from waterlogging increase from 3–11% historically to 10–20% by 2080, reflecting a trade-off between duration and timing relative to crop stage. Greater potential for waterlogging-tolerant genotypes exists in environments with longer temperate growing seasons. Altering sowing time and adopting waterlogging-tolerant genotypes reduces yield penalties by 18%, while earlier sowing of winter genotypes alleviates waterlogging by 8%. Waterlogging stress patterns under present conditions are likely similar to future ones, suggesting that adaptations for future climates could be designed using current stress patterns.

Ke Liu, Matthew Tom Harrison, Haoliang Yan, De Li Liu, Holger Meinke, Gerrit Hoogenboom, Bin Wang, Bin Peng, Kaiyu Guan, Jonas Jaegermeyr, Enli Wang, Feng Zhang, Xiaogang Yin, Sotirios Archontoulis, Lixiao Nie, Ana Badea, Jianguo Man, Daniel Wallach, Jin Zhao, Ana Borrego Benjumea, Shah Fahad, Xiaohai Tian, Weilu Wang, Fulu Tao, Zhao Zhang, Reimund Rötter, Youlu Yuan, Min Zhu, Panhong Dai, Jiangwen Nie, Yadong Yang, Yunbo Zhang, Meixue Zhou