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The frequency of summer flood events has strongly increased in Eastern Europe during the last decades. The creation of water storage areas to avoid flooding is often combined with the re-creation of more natural and biodiverse riverine systems. This urges the need to understand the consequences of summer inundation, when microbial activity is significantly higher than during winter inundation, for floodplain biogeochemistry. In order to test the interacting effects of temporal flooding, water quality and agricultural use we used a mesocosm design with sods including vegetation from an area along a tributary of the Vistula River, where water storage compartments have been planned. Concentrations of nitrate and sulphate in the flood water, expected to interfere with soil redox processes, were varied at environmentally relevant concentrations. Inundation led to increased nutrient mobilization in all treatments, particularly for phosphate which reached very high concentrations in both soil water (200–300 μmol l−1) and overlaying surface water (25–35 μmol l−1) as a result of iron reduction. The response was clearly linked to different soil characteristics like the Olsen P concentration, probably caused by varying kind of land use. Unexpectedly, the flood water quality played a less important role in the response to short-term flooding. This could partly be explained by the relatively low infiltration rate into these waterlogged soils, indicating the importance of local hydrology. The findings of this study are important to understand and predict the effects of (more frequent) summer flooding of Eastern European rivers. It also indicates that it is necessary to take into account the soil quality in assessing the consequences of planned measures on biodiversity and ecosystem functioning. [ABSTRACT FROM AUTHOR]