Declining frequency yet increasing intensity of crop waterlogging events under future climates

• Climate change shifts waterlogging risk in crop production zone. • Waterlogging intensity rising up to 2.72 cent −1 while affected area declining up to 36.1 km 2 yr −1 . • Delayed stress onset by 1.1–3.7 d cent −1 , increasingly overlapping with sensitive growth stages. • Crop phenology is the dominant driver of spatial waterlogging variability. China’s Yangtze River Basin is critical for domestic food security, yet wheat production of the region is increasingly threatened by waterlogging driven by extreme rainfall events. Here, we evaluate how the changing climate impacts on the spatiotemporal dynamics of cropland waterlogging through a novel modeling framework that integrates high-resolution hydrological simulations, generated by the Distributed Hydrology Soil Vegetation Model (DHSVM), with a crop response model, SWAGMAN Destiny (Soil Water Atmosphere and Plant Management Destiny), to capture the physiological effects of waterlogging on crops. We found a decline in total annual waterlogged area over time (8.3–36.1 km 2 per year depending on climate science), accompanied by increased waterlogging intensity and delayed onset of stress (1.1–3.7 days per century). Spatial patterns show greater uncertainty and a southward shift in waterlogging-prone areas, with sporadic waterlogging becoming more prevalent under intensified warming. While the hierarchy of influencing factors remained stable with climate change, wheat phenology (day of year) emerged as the most important factor in crop susceptibility to waterlogging, and was increasingly important over time. These findings underscore the importance of tactical selection of crop phenology such as adoption of early-maturing cultivars for mitigating yield losses bespoke to environment.