Heavy metal pollution in soil and groundwater is difficult to detect in time because of its long-term accumulation. This poses a severe hazard to the ecosystem security in polluted areas. Considering the Tongyang River Basin of the Chaohu Lake water system as the research object, various pollution evaluation methods, Geographic Information System (GIS) source analysis models, adsorption and desorption experiments, and mathematical models were used. Based on the data of the heavy metal content in the soil and river sediments in the study area, regional heavy metal pollution evaluation, spatial distribution characteristics, source identification, and lake loss analysis were conducted to evaluate the current situation of environmental pollution, pollution sources, and migration and transformation of heavy metals in the basin. The results show that the heavy metals in the soil of the basin are mainly distributed from the southwest to the northeast and the island distribution to the east of Tongyang Town. The Cd, Cu, Zn, and Pb concentrations are higher in the sediment than in the soil. The Unmix analytical model was established. The natural source of heavy metals in the Tongyang River Basin and the composite pollution source of traffic-production and life showed a high correlation. According to the one-dimensional steady-state model, the concentrations of the heavy metals are in the following descending order: Zn, Cr, Pb, Cu, Ni, and Cd. The amounts of these elements entering the lake annually are 1993.04, 1028.1, 372.47, 301.72, 308.80, and 19.46 kg, respectively (a total of 4023.6 kg).