Additional rainfall in Northern Europe due to global climate change is increasing the incidences of field flooding. Flooding causes hypoxic stress that results in a reduced capacity for photosynthesis, reduction in nutrient availability and uptake, increased production of toxic metabolites by anaerobic bacteria in the soil, and ultimately yield losses and crop death. To overcome hypoxic environmental conditions, new cultivars need to be bred and tested for waterlogging tolerance. We scored 403 winter barley cultivars from the ‘Association Genetics of UK Elite Barley’ (AGOUEB) population, taking advantage of the phenotypic changes associated with hypoxic stress. This enabled us to identify an initial set of waterlogging sensitive and tolerant cultivars. Comparative analysis of a subset of 65 cultivars exposed to waterlogging stress under field and growth cabinet environments showed variability in scores due to varying sensitivity to waterlogging over multi-season field trials. In field trials, we observed waterlogging damage resulting in reductions in biomass, grain yield and crop height. However, the effects varied between seasons and the severity of waterlogging due to differences in the topography of the field and the amount of rainfall. To overcome the seasonal variations in environmental conditions in multi-season field trials, we developed in parallel, an enhanced phenotyping method by complementing field experiments with phenotyping under controlled growth conditions. The phenotyping scoring method allows for the grouping of cultivars by sensitivity and tolerance to waterlogging, with limited variance between cultivars scored in the field and controlled conditions. Together, these two complementary approaches maximise the data available to breeders, allowing for the reliable selection of more tolerant cultivars able to grow under flooding conditions.