Context Although waterlogging is known to decrease grain yield in wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), its effect on plant N traits is still unknow. Aims This study evaluated biomass N dynamics and partitioning to grains, in wheat and barley plants subjected to waterlogging. Methods Under contrasting environmental conditions, two pot experiments exposing wheat and barley plants to waterlogging events for 15–20 days at five different developmental stages, from emergence to maturity were performed. Grain N concentration, grain N content, biomass N concentration, N utilisation efficiency (NUE) and N remobilisation were recorded. Key results Both species responded similarly to waterlogging for most N traits. Reductions in grain N content differed according to the moment waterlogging occurred. The greatest reductions (46–77% compared to the control) being for waterlogging from the beginning of stem elongation to anthesis, which also showed the highest reductions in N remobilisation, N uptake at maturity, and N partitioning to the grains, but only a slight decrease in NUE. Grain N concentration raised drastically (up to 45 mg N g DW−1) with minimal grain yields. N concentration of aboveground biomass decreased during waterlogging, recovering control values at maturity. N content at maturity was related to the total biomass. Conclusions Waterlogging differentially reduced N uptake and remobilisation to grains of wheat and barley depending on the developmental stage when water excess occurred. Implications The impact of waterlogging on N economy of wheat and barley appears indirect and predominantly related to carrying effects of the stress on carbon economy due to growth reductions.