Soil pollution is a highlighted concern of modern society, particularly in developing countries. The Drosh-Shishi valley, which is a hilly region near Afghanistan with a land area of around 15,000 km2, is situated in the south of Chitral District (Pakistan) and has a population of approximately 450,000. Nowadays, this region is being explored for soil pollution, specifically heavy metals which pose a potential risk to human health. Therefore, our main goal was to investigate possible sources of heavy metals’ spread and to assess the content levels in soil and the associated risks for human. We collected 34 representative samples from transported sediments and 31 from agricultural crops. We analyzed the soil samples for the contents of Cd, Co, Cr, Cu, Mn, Ni, Pb, and Zn using ICP-OES analyzers. These values were used to obtain the contamination factor (CF) and to estimate the potential health risk caused by heavy metals according to the USEPA dose–response model. Our results suggest that the heavy metal pollution has a geogenic source, but it is also aggregated by chemical fertilizers used in farming. Regarding levels, most of the metals except Pb showed contents above the permissible level, with CF values from moderate to high. Overall, Cu and Ni showed a significant total cancer risk (TCR > 1 × 10−4) in children. Therefore, we conclude that heavy metal pollution is causing a serious threat to humans in this area, and we recommend that authorities should make more efforts in monitoring the heavy metals content in soils to reduce potential health risks.