Climatic change has great impacts on stream catchments and their ecology. Expectations are that more extreme climate events will result in undesired flooding in stream catchments. In the Netherlands, former floodplains with a history of agricultural use are put into use again as flooding areas for the purpose of water retention. This study focuses on the effects of winter flooding on various plant site conditions in the soil, such as redox, nutrient, pH, and base status. We compared the effects on groundwater- and rainwater-dominated floodplains. Water chemistry (pH, EC, HCO3, SO4, Cl, Ca, Mg, Na, K, pCO2, NO3, NH4, and PO4) and soil nutrients (Total N and P, and bio-available P) were monitored for one year, including a 3-4 month period with winter flooding. In both floodplains no direct effect of the flood-water chemistry was detected in the pore water, because the soil pores had become saturated with groundwater or rainwater, respectively, just before flooding, flood-water did not penetrate the soil. We found that the increase in pH and ammonium concentration in the rainwater floodplain were due to changes in redox status, resulting from the completely water-filled state of the soil pores during the flooding event. Furthermore, we noticed an increase in soil nutrient contents and a shift in plant species composition in the rainwater floodplain: the vegetation included more plant species characteristic for N-richness. Finally, we conclude that winter flooding has more drastic effects on biogeochemical conditions and vegetation composition in the atmotrophic conditions characteristic for low-order subcatchments than in lithotrophic conditions in the larger, higher-order subcatchments of the stream basin. © 2007 Springer Science+Business Media B.V.