This study investigated the spatial distribution, contamination, potential ecological risks and quantities of pollutant sources of six heavy metals (HMs) in sediments of 47 rivers. The catchments of the investigated rivers are situated in Poland, but some of them are located in Slovakia, the Czech Republic, and Germany. Cluster analysis was applied to analyze the spatial distribution of Cd, Cr, Cu, Ni, Pb, and Zn in river sediments. Moran I and Getis-Ord Gi* statistics were calculated to reveal the distribution pattern and hotspot values. Principal component analysis (PCA) and positive matrix factorization (PMF) were used to identify pollution sources. Furthermore, geochemical indices and sediment quality guidelines allowed us to assess sediment contamination and potential toxic effects on aquatic biota. The results showed that in 1/3rd of the rivers, the HM pattern and concentrations indicate sediment contamination. The EF, PLI, and MPI indices indicate that concentrations were at a rather low level in 2/3rd of the analyzed rivers. Only in individual rivers may the HMs have toxic effects on aquatic biota. Spatial autocorrelation analysis using the Moran I statistic revealed a random and dispersed pattern of HMs in river sediments. PCA analysis identified two sources of HMs’ delivery to the aquatic environment. Cr, Cu, Ni, Pb, and Zn originate from point and non-point sources, while Cd concentrations have a dominant natural origin. The PMF identified three sources of pollution. Among them, urban pollution sources are responsible for Cu delivery, agricultural pollution for Zn, and industrial pollution for Ni and Cr. Moreover, the analysis showed no relationship between catchment land-use patterns and HM content in river sediments.