An important hidden source of soil heavy metal pollution was the discharge of wastewater and waste rock during mining production activities. Numerous processes could result in the buildup of heavy metals in soil, and exposure to these metals could irreversibly harm a person's health. The source, distribution and quantity of historical waste residue in a pyrite mining area were described, and the nature of the waste residue was determined based on the results of toxic leaching identification in this study. The study showed that the pH value of the leaching solution of the waste residues was less than 6. Therefore, these waste residues was the second category of general industrial solid waste. The soil around the waste residues was basically acidic. Also, the content of arsenic, cadmium and copper in farmland soil around the waste residues exceeded the screening value in the Soil Environmental Quality Standard Risk Control of Soil Pollution in Farmland (GB15618-2018). Therefore, the arsenic, cadmium and copper in the waste residue could migrate with rainwater and cause some pollution to the neighboring farmland soil. The surface water was acidic and the arsenic concentration in the surface water exceeded the standard limit. Therefore, surface water was affected by acidic wastewater. However, the impact of project wastewater on groundwater was not significant. Through the analysis of the pollution status, comprehensive treatment countermeasures and secondary pollution prevention measures for the waste residue were proposed, as well as the issues that need attention when formulating specific treatment plans, which could provide a reference for similar projects.