Waterlogging stress is one of the limiting factors influencing wheat (Triticum aestivum L.) production. Wheat tolerance to waterlogging is related to the duration of the waterlogging event, the crop development stage in which waterlogging occurs, and the sensitivity of genotype. In this paper we investigated the impact of eight waterlogging durations (from 0 to 60 days) imposed at 3-leaf and 4-leaf growth stages (∼30 and 40 days after sowing) on grain yield, grain yield components, straw and root dry weight and nitrogen concentration of grain, straw, and roots of two cultivars of wheat. The results showed that of the two cultivars, one (cv. Blasco) was tolerant to waterlogging and the other (cv. Aquilante) was sensitive, thus confirming that there are high genotypic differences in terms of tolerance to waterlogging in wheat. The sensitive cultivar showed a significant reduction in grain yield and straw and root dry weight only when waterlogging was prolonged for more than 20 days. Waterlogging depressed the grain yield of the sensitive cultivar, slowing tiller formation and consequently preventing many culms from producing spikes. It slowed down spikelet formation, consequently reducing the number of spikelets per spike, and reduced floret formation per spikelet, thus reducing the number of kernels per spike.