The heavy metal contamination at abandoned smelting sites is receiving increasing attention. This study focuses on an abandoned lead–zinc smelting site and uses several methods (such as soil sampling, geophysical exploration, and groundwater monitoring) to systematically investigate the contamination characteristics, distribution patterns, and migration mechanisms of heavy metal(loid) in soil and groundwater. A geological structure model of the study area was established through drilling data and geophysical techniques (Ground penetrating radar (GPR) and Electrical resistivity tomography (ERT)), revealing the relationships among soil resistivity, electromagnetic wave reflection characteristics, and geological structure. This study revealed that heavy metal contamination in soil was concentrated mainly northwest of the site and was closely related to historical smelting activities. The presence of heavy metal(loid)s in groundwater had a complex correlation with soil physicochemical properties and environmental elements, and its distribution was influenced by both hydrogeological conditions and soil properties. This study also investigated the effects of the soil water content (SWC) and soil hydraulic conductivity (Ks) on heavy metal(loid)s migration and reported that high SWC and Ks contribute to the dissolution and migration of heavy metals. In addition, a 3D visualization model of heavy metal contamination plumes was established via Voxler software. This model intuitively demonstrated the migration and diffusion of heavy metal(loid)s in the underground environment, offering a novel perspective on their subsurface behavior. The research results provide important information for understanding the migration of heavy metal(loid)s in soil-groundwater systems.