This paper presents the state and spatial distribution of surface sediment contamination of 77 lakes in Poland by Cr, Ni, Cd, Pb, Zn, and Cu. The analyzed lakes were located within a network of nature protection areas in the territory of the European Union (EU). Spatial distribution of the heavy metals (HMs), factors favoring the delivery/accumulation of HMs in surface sediments, and pollution sources were analyzed. The results indicate the contamination of lake sediments by HMs, but the potentially toxic effects of HMs are only found in single lakes. The spatial distribution of Cr indicates predominant impacts of point sources, while for Pb, Ni, and Zn, the impact of non-point sources. The analysis showed the presence of areas with very high values of particular HMs (hot spots) in the western part of Poland, while a group of 5 lakes with very low values of Ni, Pb, and Zn (cold spots) was identified in the central part of Poland. Principal component analysis showed that presence of wetlands is a factor limiting HMs inflow to lakes. Also, lower HMs concentrations were found in lake surface sediments located in catchments with a higher proportion of national parks and nature reserves. Higher HMs concentrations were found in lakes with a high proportion of Special Protection Areas designated under the EU Birds Directive. The positive matrix factorization analysis identified four sources of HMs. High values of HMs concentrations indicate their delivery from industrial, urbanized, and agricultural areas. However, these impacts overlap, which disturbs the characteristic quantitative profiles assigned to these pollution sources.