Soil flooding and submergence, collectively termed waterlogging, are major abiotic stresses that severely constrain crop growth and productivity in many regions. Cool-season grain legumes can be exposed to submersion both at the vegetative and reproductive stages. Limited research has been carried out on these crops with waterlogging imposed at flowering. We evaluated how waterlogging periods of 0, 5, 10, 15, and 20 d at flowering affected seed yield, biomass of shoots, roots and nodules, and N uptake of faba bean (Vicia faba L. var. minor), pea (Pisum sativum L.), and white lupin (Lupinus albus L.). Faba bean tolerated submersion better than pea and white lupin. Pea and white lupin plants did not survive 10 d of submersion, and after 5 d the seed yield, shoot and root biomass, and N uptake had more than halved. Faba bean survived 20 d of waterlogging, although seed and biomass production and total N uptake were severely reduced. Shoot dry weight and seed yield decreased linearly with the duration of waterlogging, which negatively affected seed more than the vegetative plant part weight. In all three crops waterlogging at flowering led to damage, which could not be recovered during seed filling.