Organic amendments often represent a source of trace metals (TMs) in soils, which may partly leach into the groundwater. The objectives of this study were (1) to validate Hydrus-2D for modeling the transport of Zn and Cu in an Alfisol amended with pig slurry (PS) by comparing numerical simulations and experimental field data, and (2) to model the next 50 years of TM movements under scenarios of suspended or continued PS amendments. First, between 2000 and 2008, we collected detailed Zn and Cu data from a soil profile in Santa Maria, Brazil. Two hypotheses about Zn and Cu reactivity with the solid phase were tested, considering physical, hydraulic, and chemical characteristics of six soil layers. Using a two-site sorption model with a sorption kinetic rate adjusted based on laboratory EDTA extractions, Hydrus simulations of the vertical TM transport were found to satisfactorily describe the soil Zn and Cu concentration profiles. Second, the long-term fate of Zn and Cu in the soil was assessed using the validated parameterized model. Numerical simulations showed that Zn and Cu did not present risks for groundwater pollution. However, future Cu accumulation in the surface soil layer would exceed the Brazilian threshold for agricultural soils.