The study of bottom sediments was conducted within the basins of water bodies used for recreational purposes (e.g., bathing, fishing and diving) in the Silesian Upland and its periphery in southern Poland. Various concentrations of trace elements were found in bottom sediments, reflected by the following levels: Pb (30–3020 mg/kg), Zn (142–35,300 mg/kg), Cd (0.7–286 mg/kg), Ni (10–115 mg/kg), Cu (11–298 mg/kg), Co (3–40 mg/kg), Cr (22–203 mg/kg), As (8–178 mg/kg), Ba (263–19,300 mg/kg), Sb (0.9–52.5 mg/kg), Br (1–31 mg/kg), Sr (63–510 mg/kg) and S (0.001–4.590%). These trace elements are present in amounts that usually exceed those found in other bodies of water or are sometimes even unprecedented among bodies of water in the world (e.g., cadmium—286 mg/kg, zinc—35,300 mg/kg, lead—3020 mg/kg, arsenic—178 mg/kg). It was found that bottom sediments were contaminated to varying degrees with toxic metals, metalloids and non-metals, as evidenced by the values of geoecological indicators, i.e., the geoaccumulation index (−6.31 < Igeo < 10.90), the sediment contamination factor (0.0 ≤ Cfi < 286.0), the sediment contamination degree (4.6 < Cd < 513.1) and the ratios of the concentrations found to the regional geochemical background (0.5 < IRE < 196.9). It was concluded that the presence of toxic elements (e.g., lead, zinc, cadmium, chromium, strontium and arsenic) in bottom sediments should be taken into account when classifying water bodies as suitable for recreational use. A maximum ratio of the concentrations found to the regional geochemical background of IRE ≤ 5.0 was proposed as the threshold for the permissibility of recreational use of water bodies. The water bodies used for recreational purposes in the Silesian Upland and its periphery do not meet the geoecological conditions for safe use in terms of recreation and leisure activities. Forms of their recreational use that directly affect the participants’ health (e.g., fishing and the consumption of fish and other aquatic organisms) should be abandoned.