It is crucial for effectively controlling potentially toxic element (PTE) pollution to understand the pollution situation, ecological risks, health risks, and migration patterns of PTEs. However, currently, no research has been conducted on the migration patterns of soil PTEs from coal mining subsidence areas to waterlogged areas under different restoration modes. In this study, a total of 15 sediment samples and 60 soil samples were collected from landscaped wetlands, aquaculture wetland, fish–photovoltaic complementary wetland, photovoltaic wetland, and waterlogged areas with untreated coal mining subsidence. The PTE pollution status, ecological risks, health risks, migration patterns, and the important factors influencing the migration were analyzed. The results indicated that the comprehensive pollution level of PTEs in waterlogged areas with coal mining subsidence can be reduced by developing them into landscaped wetlands, aquaculture wetlands, fish–photovoltaic complementary wetlands, and photovoltaic wetlands. Additionally, the closer to the waterlogged area, the higher the Cu content in the subsidence area soil is, reaching its peak in the waterlogged area. The Cd was influenced positively by SOC and pH. The research results were of great significance for formulating reclamation plans for waterlogged areas and controlling PTE pollution.