This study aimed to determine sediment contamination in the Beidagang Wetland Nature Reserve to describe atmospheric deposition of trace metals. We analyzed Hg, Cd, Pb, TOC, TN, TP, δ13C, and δ15N, and studied their variations in surface sediments and in the vertical profiles of sediment cores collected from the reserve. Evaluation of environmental trace metal contamination using sediment quality guidelines and geochemical background values indicated that the risk of metal pollution in the reserve sediments was relatively low. Concentrations of Hg, Cd, and Pb in the sediments were much lower than concentrations in sediment samples from Bohai Bay and polluted rivers in Tianjin. Enrichment factors indicate that samples are moderately contaminated with Hg, Cd, and Pb; whereas the geo-accumulation index results classify the sediments as uncontaminated to moderately contaminated with Hg, Cd, and Pb. The distribution patterns of trace metal concentrations in the three core samples were uniform. δ13C and δ15N were used to track the sources of TOC and TN in sediments. Results show that TOC mainly originated from the residue and decaying matter of aquatic plants (e.g., algae, reeds, and Typha), while TN was derived from soil N and elevated atmospheric N deposition. Because domestic and industrial waste is not discharged into the Beidagang Wetland Nature Reserve, trace metals found in sediments mainly originate from atmospheric deposition. The results provide baseline data for analysis of trace metal accumulation in Beijing-Tianjin-Hebei, a region subject to atmospheric deposition in northern China.