The distribution and species richness of aquatic molluscs were analysed within a 186-km-long section of a large (755-km-long) lowland river floodplain using GIS maps. Special attention was paid to threatened species. An attempt was made to identify local ‘hotspots’ of molluscan diversity and to determine the most important areas for conservation based on species richness, number of threatened species and indices of synthetic conservation (Q) and centres of population density (ICD). Over four years of investigation, carried out in 176 water bodies, a rich malacofauna was identified: 58 species including 20 of elevated conservation concern. GIS maps revealed numerous ‘hotspots’ of mollusc species richness and higher incidence of threatened species, as well as areas characterized by raised Q and ICD indices. Water body size and hydrological connectivity positively influenced species richness and Q values. The highest values of these variables were found in large water bodies having limited surficial connectivity with the river channel. Species richness, numbers of threatened species, and Q and ICD values were significantly higher in younger permanent water bodies compared with semi-permanent or temporary ones representing advanced successional stages. Spatial visualization data collected in the study area indicate that the most valuable sites for the conservation of aquatic molluscs include both sides of the river in the lower part of the middle stretch of the lower Bug River valley. Copyright © 2013 John Wiley & Sons, Ltd.