The objectives of our survey were to determine the most important environmental factors within buffer zones that influenced mollusc communities and to evaluate the ecological conservation value of natural aquatic habitats (NAHs) that support mollusc species. Analysis of the spatial structure of buffer zones and catchments was based on a set of landscape metrics. Land cover classes were determined, and buffer zones within a radius of 500 m from a sampling point were marked out. Mollusc samples were collected from each NAHs. Our results showed that the number of patches and mean patch size were most associated with the distribution of mollusc species. Within patches of buffer zones, the length of the catchment boundaries with low-density housing, an increasing area of forest and pH of the water were also significant. Our results proved that landscape metrics provide essential information about catchment anthropogenic transformation. Therefore, landscape metrics and the designated buffer zones should be included in restoration plans for the river, water bodies and adjacent habitats as elements of modern, sustainable water management. NAHs located along a valley of a lowland river provide refuges for molluscs, play an essential role in the dispersal of IAS, create important protective biogeochemical barriers for rivers, constitute necessary sources of moisture and water and support microhabitats for distinct mollusc communities, especially in the context of global warming.