The application of pig slurry to soil can result in the accumulation of soil Cu and Zn, alter soil Cu and Zn fractions, and result in soil, surface water, and subsurface water contamination. This study evaluated the accumulation and distribution of Cu and Zn in soil profiles from 10 areas treated with pig slurry for 3–30 yr. A microwatershed within the municipality of Braço do Norte in the state of Santa Catarina and in the southern region of Brazil was studied. Hapludalf soil samples were collected at depths of 0.0–0.05, 0.05–0.10, 0.10–0.20, 0.20–0.30, and 0.30–0.40 m from 10 areas where pig slurry had been applied for 3–30 yr. The soil samples were dried, prepared, and analyzed to determine their chemical characteristics, particularly to quantify their Cu and Zn fractions. Although long-term pig slurry application resulted in greater available Cu and Zn concentrations in the surface soil layer, the migration of available Cu in the soil profile only occurred in areas that were subjected to more than 17 yr of slurry application. The application of pig slurry increased the available Cu and Zn contents in the surface soil layer; however, the available Cu in the soil profile increased in the areas with more than 17 yr of slurry application. Cu accumulation mainly occurred in the organic and mineral soil fractions, and Zn accumulation mainly occurred in the mineral fraction. Overall, Cu posed a greater risk for surface water contamination than Zn, especially in areas with more than 17 yr of pig slurry application.