Infrequent inundations of river floodplains during the growing season are known to have a stronger impact on plant distributions than annual flooding in the winter and early spring. Growing season responses to flooding may be explained by 1) direct effects of flooding on fully developed plants, and/or 2) indirect effects on vegetation mediated by soil nutrient availability. Nutrient availability, in turn, is the result of the effects of summer flooding on the microbial community that reacts to changes in soil moisture conditions. We employed a mesocosm experiment to test these ideas. Soil monoliths were obtained from a highly modified floodplain on the river Rhine (Netherlands) and a more pristine floodplain on the river Narew (Poland). Vegetation performance and soil nutrient availability were measured in the monoliths, which were exposed to a 14-day summer inundation. Flooding had a negative effect on plant biomass in the Dutch soils, while biomass remained unchanged on soils from the pristine Polish floodplain. This is probably related to the absence of summer flooding in the Dutch floodplains due to intensive river regulation the last century. Summer flooding is still common in the Polish situation where more original hydrology patterns remained. One month after 14-day inundation there was a decrease in species diversity (Shannon's H) in both systems. This decrease was caused by better performance of a few graminoid species. Pore water phosphate concentrations were higher in Dutch soils and reached the highest levels during inundation. Nitrate concentrations were also generally higher in the Dutch mesocosms, although during inundation concentrations were very low in both soil types. Differences in nutrient availability between soils were reflected in aboveground biomass tissue concentrations, yet biomass response was apparently not related to nutrient availability. We conclude that ecological rehabilitation in the Netherlands, i.e., return to a more natural hydrology, resulting in an increased incidence of summer inundation could lead to a short-term reduction in productivity and changes in patterns of species abundance and dominance.