We investigated sediments from 23 lakes situated in northeastern Poland and analyzed them for major constituents and selected heavy metals. Short sediment cores were collected from the deepest parts of the lakes, and subsequently, a surface layer (0-2 cm) and reference layer (50-52 cm) were sampled from each. In the collected samples, the content of the major constituents (organic matter, carbonates, and minerogenic material) and chosen heavy metals (Cd, Cu, Ni, Pb, and Zn) was analyzed. In the reference layer, representing natural metal content, we identified quite a substantial diversity among lakes, making it difficult to pinpoint one geochemical background value for the whole region. A multivariate analysis of the interrelationships among elements and a comparison of the median values revealed no statistically significant differences between surface and reference levels. The ratio of the mean content in the surface and reference sediments ranged from 0.9 to 1.6, indicating the lack of or only slight anthropogenic pollution in surface sediments. From a spatial perspective, higher metal contents were observed in the eastern part of the study area, but this trend manifested in both surface and reference sediments. Thus, the inference is that the recently accumulated sediments are characterized by a content that is representative of the natural geochemical background for the selected metals.