Abandoned Pb/Zn smelters are often accompanied by a large amount of smelting slag, which is a serious environmental problem. Previous studies have demonstrated that slag deposits pose an environmental threat even if the smelters are shut down. Herein, a Pb/Zn smelter and its impacted zone in GeJiu, Yunnan, China were selected as the study area. The risk and source apportionment of heavy metals (HMs) in the soil of the impacted zone were systematically studied. Based on the hydrogeological features, the migration path and output fluxes of the HMs released from smelting slag to the impacted zone were investigated. The HM contents (Cd, As, Zn, Pb, and Cu) in the soil substantially exceeded the screening values of the Chinese soil standard (GB15618-2018). Based on the results of the Pb isotopic and statistical analyses for source apportionment, the contaminated sites and agricultural irrigation water had a large impact on the HMs of soil. The hydrological analysis results showed that runoff, as an HM migration path under rainfall, continued to affect the environment. The water balance calculations using the Hydrologic Evaluation of Landfill Performance model showed that the rainfall was distributed on site as follows: evaporation (57.35%), runoff (32.63%), and infiltration (10.02%). Finally, the output fluxes were calculated in combination with the leaching experiment. As, Zn, Cd, Pb, and Cu runoff had the output fluxes of 6.1 × 10⁻³, 4.2 × 10⁻³, 4.1, 1.4 × 10⁻², and 7.2 × 10⁻⁴ mg/kg/y, and infiltration of 1.9 × 10⁻³, 1.3 × 10⁻³, 1.3, 4.0 × 10⁻⁴, and 2.2 × 10⁻⁴ mg/kg/y, respectively. Therefore, this study offers theoretical and scientific recommendations for effective environmental management and engineering remediation.