Abstract. Raising safety levees and reinforcing dykes is not a sufficient and sustainable solution to the intense winter and summer floods occurring with increasing frequency in Eastern Europe. An alternative, creating permanently flooded floodplain wetlands, requires improved understanding of ecological consequences. A 9 month mesocosm study (starting in January), under natural light and temperature conditions, was initiated to understand the role of previous land use (fertility intensity) and flooding water quality on soil biogeochemistry and vegetation development. Flooding resulted in severe eutrophication of both sediment pore water and surface water, particularly for more fertilized soil and sulphate pollution. Vegetation development was mainly determined by soil quality, resulting in a strong decline of most species from the highly fertilized location, especially in combination with higher nitrate and sulphate concentrations. Soils from the less fertilized location showed, in contrast, luxurious growth of target Carex species regardless water quality. The observed interacting effects of water quality and agricultural use are important in assessing the consequences of planned measures for ecosystem functioning and biodiversity in river floodplains.