River-lake systems most often behave as hydrographic units, which undergo complex interactions, especially in the contact zone. One such interaction pertains to the role of a river in the dispersal of trace elements carried into and out of a lake. In this study, we aimed to assess the impact of rivers on the accumulation of heavy metals in bottom sediments of natural lakes comprised in postglacial river-lake systems. The results showed that a river flowing through a lake is a key factor responsible for the input of the majority of available fraction of heavy metals (Zn, Mn, Cd and Ni) into the water body and for their accumulation along the flow of river water in the lake. The origin of other accumulated elements were the linear and point sources in catchments. In turn, the Pb content was associated with the location of roads in the direct catchment, while the sediment structure (especially size of fraction and density) could have affected the accumulation of Cr and Zn, which indicated correlations between these metals and fine fraction. Our results suggest that lakes act as filters and contribute to the self-purification of water that flows through them. As a result, the content of most metals in lake sediments showed a decrease by approx. 75% between the upstream (inflow) and downstream (outflow) sections. The increased content of two metals only, such as chromium and cadmium (higher by 2.0 and 2.5 times, respectively, after passing through the lake), was due to the correlation of the metals with fine sand. Both the content and distribution pattern of heavy metals in lake sediments are indicative of the natural response of aquatic ecosystems to environmental stressors, such as pollutant import with river water or climate change. The complex elements creating the water ecosystem of each lake can counteract stress by temporarily removing pollutants such as toxic metals form circulation and depositing them mostly around the delta.