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Fluctuations of the water level at the edges of temporary water bodies provide favourable living conditions for annual plant communities of the phytosociological class Isoëto-Nanojuncetea. Such communities of periodically flooded ponds within the agricultural landscape of NE Germany are particularly rich in rare plant species of that class. During the past decades drainage, fertilisation and herbicides in the surrounding arable fields have led to a severe decline in diversity of these species. To develop efficient conservation strategies it is essential to understand the factors driving the species composition. Therefore, we studied how varying water regimes, soil properties and agricultural practices affect the diversity and species composition of these temporary ponds. The study was carried out in seven ponds on a conventionally managed farm in NE Brandenburg. At each of these wetlands mixed soil samples were taken to determine the pH, total nitrogen and phosphorus concentration. The plant species were recorded in 177 plots, each covering 1 x 1 m2. For each plot, the water level was recorded in April, July and August 2013, respectively, resulting in five "water level regimes". Total species number and percentages of Isoëto-Nanojuncetea species were determined per plot, to evaluate water level effects on the vegetation. In addition, mean Ellenberg indicator values for light, moisture and nutrients were calculated to assess the environmental conditions.