Recent climate analyses show trends for increasing precipitation variability with increasing precipitation sums in Mali. The increasing occurrence of temporary intra-seasonal droughts and waterlogging longer than a week demands climate-smart solutions. Research has focused on water deficits since the 1980s. However, besides droughts, waterlogging can restrict productivity of sensitive cash and staple crops as cotton and corn. The year 2019 offered the historically unique opportunity to monitor waterlogging effects with 1088 mm precipitation in the rural commune Cinzanawith an isohyet of 681 mm. Impacts of two extreme downpours on three sorghum cultivars were monitored in a farmers-field experiment with three replications. All sorghum cultivars performed well in 2019 with significantly higher grain and above ground biomass yields than in the reference year 2007, with well distributed rainfall in Cinzana. “Jakumbè” (CSM63E) produced significantly higher grain yields than the hybrid cultivar “PR3009B” bred for high harvest index. The local cultivar “Gnofing” selected by local farmers produced significantly higher above ground biomass. All cultivars tolerated without severe stress symptoms 20 days waterlogging and 72 h inundation. Further waterlogging resilience research of other crops and other sorghum cultivars is needed to strengthen food security in Mali with expected increasing precipitation variation in the future.