Improving our understanding of how different tree species function in urban stormwater management systems is important, as tree pits may provide a temporary reservoir for stormwater and as trees have the potential to actively reduce stormwater runoff by transpiration. While urban tree planting pits are increasingly used for short-term water storage during stormwater runoff events, this storage can have negative effects on both tree vitality and water removal capacity, since stress from waterlogging result in stomatal closure. However, sensitivity to water stress varies by species. It is therefore important to determine which tree species can maintain long-term vitality and continued transpiration even under water stress, and thus are suitable for such locations. Here, we studied how nine different tree species, varying in expected tolerance to water stress, were affected by short-term and seasonal waterlogging, in a greenhouse experiment. The seedlings (Magnolia x loebneri, Tilia tomentosa, and Sorbus torminalis – low water logging tolerance; Cercidiphyllum japonicum, Rhamnus cathartica, and Fraxinus ornus – medium water logging tolerance; Quercus palustris, Acer saccharinum, and Fraxinus pennsylvanica – high water logging tolerance) were exposed to two days, five days and seasonal waterlogging. The treatments reflected best practice (optimal), suboptimal and total lack of tree pit drainage, using Swedish standards. Stomatal conductance and leaf water potential were determined regularly over a period of 71 days, and morphological adjustments were registered. Four of the species were affected already after two days of waterlogging, with reduced stomatal conductance either during the waterlogging or immediately after, and only the most waterlogging tolerant species were unaffected by the five-day treatment. However, all plants survived waterlogging for almost 30 days before the estimated permanent wilting was reached in some plants. We suggest that tree species selection for stormwater management systems should consider the species’ capacity to maintain high stomatal conductance during waterlogging, as there were clear differences between species. The effectiveness of the selected species could have an important impact on the stormwater management capacity of cities, as well as on other aspects of ecosystem service delivery from urban trees.