Longitudinal organisation of macroinvertebrate fauna along river is one of the most important problem commonly used to explain the functioning of flowing water ecosystems. The river system can be treated as a mosaic of landscapes patches and riverine macroinvertebrates' community structure is a function of longitudinal changes in its key abiotic patterns. The aims of the study was to analyse the taxonomic structure of molluscs in the river-lake system, to compare river and lake malacofauna and to determine the factors responsible for its diversity in lakes and river stretches. The study based on comprehensive analysis of malakofauna sampled at 10 sites in the Krutynia River and in all 19 lakes it flows through were performed in the years 2008–1011. River Krutynia is one of the most important rivers in Masurian Lakeland (north-eastern Poland) with length of 100 km and mean annual discharge of 10.6 m³ h^-1. It forms a characteristic river-lake system typical for the lakeland landscape in Central Europe. The density and taxonomic composition of molluscs were found as strongly dissimilar in a local scale — between closely located lakes and between particular parts of flowing waters, divided by the lakes. Multivariate methods were used to demonstrate a clear dissimilarity of lake and river malakofauna and to show that the mean content of phosphorus, nitrogen and organic matter in bottom sediments were correlated with each other in lakes but not in the river. The most important species differentiating river sites into larger groups with respect to the similarity was Theodoxus fluviatilis while Stagnicola corvus and Anisus vortex were such species differentiating lakes. The numbers and percentages of Dreissena polymorpha and Unionidae were negatively correlated with nutrients in river sediments. There was a strong positive relationship between nutrients' concentrations in sediments and the percentages of Viviparus, Obtained results of multiple regression indicate a strong effect of nutrient and organic matter concentrations in the sediments and the distance from the site to the lake on the domination structure of molluscs.