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Agricultural soils originating from carbonate rocks within karst regions exhibit inherent high concentrations of potentially toxic elements (PTEs) due to geogenic processes. However, the influencing factors of the elevated levels of PTEs in the naturally contaminated karst regions remain inadequately comprehended. This research investigates the chemical compositions of 278 soils derived from carbonate rocks. Descriptive statistics, stepwise multiple regression, and the random forest (RF) method were applied to screen the significant factors that affect the distribution, migration, and enrichment of the PTEs in soils. Cadmium (Cd) and arsenic (As) are the most highly contaminated PTEs in the soils of the study area, and the average contents of Cd and As in soils are 11.5 and 2.92 times the national soil background value, respectively. The pollution risk ranking of PTEs is Cd > As > Cr > Zn > Pb > Cu > Ni > Hg, using the proportion exceeding the risk screening thresholds of agricultural land as the standard. Soil Fe2O3 and Mn contents, soil pH and total organic carbon (TOC) values, and weathering intensity (characterized using the chemical index of alternation, CIA) are the most important factors influencing the PTE levels in agricultural soils. [ABSTRACT FROM AUTHOR]