This research aimed to evaluate the residual Cu and Zn in tropical soil over 21 years after amendment with industrial waste, lime, and compost. Soil samples were collected from a well-maintained experimental field amended one time with industrial waste high in Cu and Zn set in 1998 at about 1.5–20 years after amendment. Treatments were arranged in a randomized block design with a metal-wares industrial waste at rates 0, 15, and 60 Mg·ha−1, lime at 0 and 5 Mg·ha−1, and compost at 0 and 5 Mg·ha−1. Soil samples were also taken vertically in the exact plot centers at depths of 0–75 cm of plots not amended with lime and compost and also from topsoils (0–15 cm) at 90 points with distances 50 cm between each other in each of the respective plots 21 years after amendment. Significant increases in Cu and Zn caused by waste were observed over 21 years. The increase in soil pH by lime was observed over 10 years but its effect in decreasing Cu and Zn was observed only at 1.5 years, particularly in topsoils. However, the effect of lime in lowering Cu and Zn was observed over 20 years when waste and/or compost were also given. Similarly, the effect of compost was absent over 20 years but significant when waste and/or lime were also given. The relative concentration of Cu and Zn in the 60 Mg waste ha−1 plots decreased over 20 years to 17–53% for Cu and to 12–33% for Zn; their concentrations were, in general, lower with lime and/or compost addition. The relative concentrations of Cu and Zn significantly decreased over 21 years in plots with 15 or 60 Mg·ha−1 and increased in the control plots. Heavy metals moved in soil significantly through soil tillage and erosion and partially by leaching.