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Increased risk of soil waterlogging in winter and spring at northern latitudes will potentially affect forest production in the future. We studied gas exchange, chlorophyll content index, chlorophyll fluorescence, nutrient concentration and biomass accumulation in 1-year-old silver (Betula pendula Roth) and pubescent birch (Betula pubescens Ehrh.) seedlings. We hypothesized that B. pubescens has different physiological mechanisms that make it tolerate waterlogging better than B. pendula. The treatments were: (i) no waterlogging throughout the experiment; (ii) 4-week waterlogging during dormancy (dormancy waterlogging 'DW'); (iii) 4-week waterlogging during the early growing season (growth waterlogging 'GW'); and (iv) 4-week DW followed by 4-week GW during the early growing season ('DWGW'). Stomatal conductance and light-saturated net assimilation rate were reduced by GW in both species, and in B. pubescens also by DW. However, recovery was seen during the follow-up growing season. In B. pendula, DW, GW and DWGW temporarily resulted in reduced stem biomass, and GW and DWGW caused reduced leaf biomass. In B. pubescens, the stem biomass was decreased in GW and DWGW. Leaf nitrogen (N) and phosphorus (P) concentrations were generally low, and increased by GW, while potassium, calcium, magnesium and to some extent, boron and zinc concentrations decreased in both species and additionally manganese in B. pendula. The increases in N and P are mostly due to a concentration effect due to smaller leaf biomass, yet suggest that their uptake was not impaired. The decreases in cation concentrations are likely to be connected to impaired root functioning, which was not yet fully recovered from GW. We conclude that morphological acclimation to waterlogging of the leaves and roots rather than photosynthesis explains why B. pubescens is able to grow better in wetter areas than B. pendula. [ABSTRACT FROM AUTHOR]