In-crop soil waterlogging caused by extreme rainfall events, high ground water tables, excessive irrigation and lateral ground water flow inhibit potential grain yields. However, the extent to which yield is influenced by the timing and duration of waterlogging relative to crop phenology is unknown. To investigate this, we conducted various waterlogging treatments on a range of modern barley genotypes varying in their waterlogging tolerance, with tolerance conferred through aerenchyma formation under oxygen deficit conditions. Results showed that yield was reduced by 35% in W1 (waterlogging at Zadoks stage (ZS) 12.5 for one month) to 52% in WL3 (waterlogging at ZS 15 for two months) due to fewer spikes/m2 and kernels/spike. Two weeks waterlogging at ear emergency stage had the greatest impact on yield (70% reduction) due to its effect on spikelet fertility and grain filling. Phenology was delayed 1-8 ZS at the end of waterlogging treatments, with the waterlogging-susceptible cultivar Franklin showing the greatest delays, and waterlogging tolerant genotypes capable of AF (Macquarie+, TAMF169) having the least delays (0-4 ZS). Genotypes with the AF QTL (Macquarie+) showed a slight and nonsignificant yield reduction compared with unwaterlogged controls and mitigated around 23% yield loss under early phenological waterlogging stress.