The highest freshwater mollusc diversity was repeatedly found in lowland standing waters. Despite the increasing degradation of these habitats and spreading of non-native species, still only little is known about the main drivers of mollusc diversity among individual stagnant water bodies at regional scale. Besides environmental filters, freshwater mollusc distribution depends on the occurrence of active vectors and interconnection among individual sites due to passive dispersion mode of molluscs. Further, the distance between sites and presence of stepping stones governs the success of mollusc migration to new habitats, being also link with their long-term survival in a dynamic environment. The presence of rare mollusc species can thus indicate low anthropogenic pressure and the quality of site. We quantitatively sampled mollusc assemblages at 56 stagnant water bodies within 5,000 ha region in the Dyje River floodplain (south-east Czechia). It total, 33 species were found, with the maximum number of 15 species (5 on average per site). By measuring an extensive set of environmental predictors we were able to describe the main variation in species composition of local assemblages. This allows to compare the effect of environmental based processes and distance based processes on metacommunity structuring of mollusc assemblages in standing waters of a lowland agricultural region.