The aim of this study was to analyze the heavy metals transport in a river-reservoir system. Sediment samples from 25 locations (9 from the Powa River and 16 from the Stare Miasto Reservoir) were analyzed for trace metals contents (Cr, Ni, Cu, Zn, Cd, and Pb). The relationships between heavy metal concentrations and bottom sediment physical properties were determined with the use of the multivariate statistical techniques cluster analysis (CA), principal component analysis (PCA), and canonical correspondence analysis (CCA). The results showed that concentrations of heavy metals in the sediments of the reservoir were higher than those in the bottom sediments of the river. Concentrations of heavy metals in bottom sediments in the river above the reservoir were characterized by lower spatial variability. Decisive influence on heavy metal concentrations of bottom sediments had silt, clay, and total organic matter content.