Exogenous sources and the superposition effect of HMs in agricultural soils made the idenfication of sources complicated in a karst area. Here, a typical watershed, a research unit of the karst area, was chosen as the study area. The smaller-scale study of watersheds allowed us to obtain more precise results and to guide local pollution control. In this study, sources of HMs in agricultural soil were traced by a CMB model. Superposition effects were studied by spatial analysis of HMs and enrichment factor (EF) and chemical fraction analysis. The average concentrations of Cd, Pb, Cr, Cu, Ni and Zn in surface soils were 8.71, 333, 154, 51.7, 61.5 and 676 mg∙kg−1, respectively, which exceeded their corresponding background values. The main sources of Cd, Pb and Zn in agricultural soil were rock weathering, atmospheric deposition and livestock manure, and their contributions were 47.7%, 31.0% and 21.2% for Cd; 7.63%, 78.7% and 13.4% for Pb; and 17.0%, 52.3% and 28.1% for Zn. Cr mainly derived from atmospheric deposition (73.8%) and rock weathering (20.0%). Cu and Ni mainly came from livestock manure (81.3%) and weathering (87.5%), respectively, whereas contributions of pesticides and fertilizers were relatively limited (no more than 1.04%). Cd, Pb, Zn and Cu were easily enriched in surface soils near the surrounding pollution sources, whereas Cr and Ni were easily enriched in the high-terrain area, where there was less of an impact of anthropogenic activities. The superposition of exogenous sources caused accumulation of Cd, Pb and Zn in topsoil, contaminated the subsoil through leaching and improved bioavailability of Cd and Pb, causing high ecological risk for agricultural production. Therefore, Cd and Pb should be paid more attention in future pollution control.