Deep shade and waterlogging are two common stressors affecting seedling performance in the understorey of evergreen rainforests. It has been hypothesised that high levels of carbon storage confer shade- and waterlogging tolerances by preventing carbon limitation under such stresses. Whether the tolerance to both stresses is positively or negatively related remains unclear. To explore the role of carbon storage in the relationships of waterlogging and shade tolerance, we investigated the responses to waterlogging and the levels of carbon storage in two species pairs with contrasting shade tolerance: Embothrium coccineum J.R.Forst.&G.Forst. and Gevuina avellana Mol. (Proteaceae) and Nothofagus dombeyi (Mirb.) Oerst. and Nothofagus nitida (Phil.) Krasser (Nothofagaceae). We subjected seedlings to waterlogging or control conditions for 30 days and evaluated survival, relative growth rate (RGR), biomass distribution, leaf chlorophyll fluorescence (Fv/Fm), and concentrations of total soluble sugars, starch and non-structural carbohydrates in different plant tissues. Waterlogging reduced survival, Fv/Fm and RGR in all species; however, the magnitude of reduction of Fv/Fm and RGR was significantly higher in the shade-intolerant species than in their shade-tolerant counterparts. In general, shade-intolerant species had significantly higher non-structural carbohydrate concentrations in waterlogging than in control conditions. By contrast, shade-tolerant species had similar non-structural carbohydrate concentrations under both conditions. Our results indicate that relatively shade-tolerant species performed better under waterlogging. A reduction in non-structural carbohydrates under waterlogging was not observed in any of studied species; rather, shade-intolerant species exhibited non-structural carbohydrate accumulation suggesting that carbon storage does not confer waterlogging tolerance in these species.