Wetlands are recognized as one of the most important natural environments for humans. At the same time, heavy metal pollution has an important impact on wetlands. China's Raoyanghe Wetland is one of the most important natural wild species gene banks in China. Eight heavy metal elements (As, Cd, Cr, Cu, Hg, Ni, Pb, and Zn) in surface layer and deep layer soils were analyzed using statistical-, pollution index-, and Nemerow index-based methods, the Hakanson potential ecological risk index method, and principal component and cluster analyses. The results showed that the maximum concentrations of heavy metals exceeded the background values in the core area and buffer zone of the wetland, but the heavy metal content of the soils was generally low and did not exceed 30%. With the exception of Hg, heavy metal concentrations showed strong spatial differentiation. The differences between the surface layer and deep layer soils of the core area were smaller than in the buffer zone. With the exception of Cd, a clear vertical zonation in the buffer zone soils was observed, showing greater evidence of external influences in this zone than the core. With the exception of partial surface soils, which indicated a safe level of pollution in the core area, all other soils were classified as having a ‘mild’ level of pollution. Thus, the wetland is moderately polluted, with both the core area and the buffer zone presenting a low level of potential ecological risk. According to the results of the present study, heavy metal contaminants in the wetland soils were found to be derived mainly from the natural sources.