This study aimed at investigating the distribution of heavy metals (HMs: Zn, Pb, Cd, Ni, Cr, and Cu) in the bottom sediments of 28 reservoirs covered area of Poland. The paper evaluates the pollution of sediments with HMs and their potential toxic effects on aquatic organisms and human health on the basis of results provided by the Chief Inspectorate of Environmental Protection in Poland. The average concentrations of HMs in the bottom sediments of the reservoirs were as follows: Cd < Ni < Cr < Cu < Pb < Zn. (0.187, 7.30, 7.74, 10.62, 12.47, and 52.67 mg∙dm−3). The pollution load index values were from 0.05 to 2.45. They indicate contamination of the bottom sediments in seven reservoirs. The contamination-factor values suggest pollution with individual HMs in 19 reservoirs, primarily Cr, Ni, Cu, and Pb. The analysis showed that only two reservoirs had the potential for toxic effects on aquatic organisms due to high concentrations of Cd and Pb. The hazard index values for all the analyzed HMs were less than one. Therefore, there was no non-carcinogenic risk for dredging workers. The reservoirs were divided into two groups in terms of composition and concentration values. Reservoirs with higher concentrations of HMs in bottom sediments are dispersed, suggesting local pollution sources. For the second group of reservoirs, HMs’ concentrations may be determined by regional pollution sources. The analysis showed that Pb, Zn, and Cd concentrations are higher in older reservoirs and those with higher proportions of artificial areas in their catchments. Concentrations of Ni, Cu, and Cr are higher in reservoirs in south Poland and those with higher Schindler’s ratios.