Water level fluctuations (WLF) can be important disturbances promoting the diversity of riparian plant communities, but are currently absent from many managed aquatic ecosystems. A lack of WLF is thought to reduce plant diversity and hamper hydrosere succession. However, a positive impact of WLF on plant diversity may crucially depend on nutrient availability and the presence of a potential ecosystem engineer, the floating plant Stratiotes aloides, that may provide structural support to riparian plants. We tested the interactive effects of 40 cm flooding, presence of S. aloides and sediment nutrient availability (N and P) on growth and horizontal expansion of eight wetland plant species in a 10 week experiment. Seven out of eight species showed a significant elongation response to flooding. Compared to stagnant water levels, flooding in combination with high nutrient availability decreased horizontal expansion in two short species and increased it in two tall species, whereas flooding decreased horizontal expansion in two other short species under both nutrient levels. In this 10 week experiment, we observed no effect of S. aloides on the measured plant parameters. This experiment shows short-term negative effects of flooding on most of the short species. On the long-term, we hypothesize that improvements in water quality and seedling recruitment due to drawdown may result in net positive effects of WLF in the riparian zone, but as the species that were rare in the field happened to be short, care should be taken to maintain rare species when allowing more WLF.