Surface samples (0–25 cm each) of agricultural soils were investigated in five Regions (voivodeships) of southern Poland. The mean Potentially Harmful Element (PHE) pseudototal content ranges were as follows (mg/kg): As 5.19–10.9, Cd 0.34–1.56, Co 1.92–6.70, Cr 9.05–25.7, Cu 8.74–69.4, Hg 0.001–0.08, Ni 3.93–19.9, Pb 20.3–183, Sb 0.80–1.42, Tl 0.04–0.17, and Zn 61.3–422. The PHE availability depended on pH, the organic carbon (Corg) content, and the pseudototal PHE content in soils. Exchangeable and acid soluble PHE contents (BCRF1) determined in the Community Bureau of Reference (BCR) three-step sequential extraction procedure decreased in this order: Cd > Zn > Co > Ni = Sb > Cu > Tl > As > Cr = Pb. Actually available PHE contents in pore water (0.01 mol/dm3 CaCl2) ranged as follows: Cd 0.81–17%, Cr 0–0.25%, Cu 0.01–2.31%, Ni 0.16–2%, Pb 0.2–0.49%, and Zn 0.25–2.12%. The potential soluble total content of PHEs in pore water (0.05 mol/dm3 Na2EDTA) ranged as follows: Cd 27–91%, Cr 0.7–7.1%, Cu 6.7–98%, Ni 3.6–41%, Pb 15–41%, and Zn 3–34%. The mobility factor (MF) values indicated Cd (31.6%) and Zn (21.0%) as the most mobile elements in soil. Other PHEs followed the order of Co > Ni > Tl > As > Sb > Cu > Cr > Pb, with the MF values <10%. The risk assessment code (RAC) values revealed a very high ecological risk of Cd and Zn in the Podkarpackie Region and a high ecological risk of Cd in the Regions of Opolskie, Śląskie, Małopolskie, and Podkarpackie, and the same of Zn in the Opolskie and Śląskie. The modified risk assessment code (mRAC) index pointed a very high potential of adverse effects in soils in the Podkarpackie and a medium potential in the Opolskie, Śląskie, Małopolskie, and Świętokrzyskie. The potential adverse effect risk, described by the individual contamination factor (ICF) factor, was the following in the Regions, in the decreasing order: Cd > Pb > Sb > Zn > Co > Cu > Ni > Tl > As > Cr, and the same as described by the global contamination factor (GCF) values: Opolskie > Podkarpackie > Świętokrzyskie > Śląskie > Małopolskie.