The concentrations of toxic metals (TM) were analyzed in 498 samples of agricultural soils used for intensive vegetable cultivation in the watershed of Barracão dos Mendes, Brazil. The goal of this study was to characterize the distribution of these elements and the main natural and anthropogenic factors affecting their accumulation. In general, the average concentrations of TM were higher than the reference quality values for cultivated soils in the region, with the exception of Cr, Co, Ni and Mn, and the average concentration of Cd was ten times greater. Three sources of variation in the distribution of TM concentrations were identified: one related to topographic relief, another related to lithology, and one related to the massive use of agrochemicals. These factors contributed to TM accumulation in the soil; moreover, the transport of toxic metal-enriched clay by runoff resulted in higher concentrations of these elements in the lower parts of the slope. The long-term application of massive amounts of fertilizers and pesticides resulted in the accumulation of Cr, Cu, Zn, Ni, Pb and Cd in the vegetable cultivation soils and promoted the enrichment of macronutrients, mainly P and K. Moreover, the spatial distribution of TM in the agricultural soils of this mountain agroecosystem was affected by intensive vegetable cultivation, which altered the natural TM distribution dynamics determined by variations in topographic relief and lithology. In intensive cultivation areas, the TM distribution was also influenced by soil management practices such as tillage along the slope direction and massive mineral and organic fertilization.