The present study was emphasized to evaluate the pollutant levels of the sediments of Yundang Lagoon, at Western Xiamen Bay, Xiamen, China. Xiamen island is one of the most rapid developing and urbanizing cities in China. Bottom surface sediments of 18 locations of Yundang Lagoon including inlet channel, outlet channel and upstream lakes were collected to evaluate the contamination, spatial distribution, risk and possible sources of heavy metals including Chromium (Cr), Manganese (Mn), Nickel (Ni), Copper (Cu), Zinc (Zn), Arsenic (As), Cadmium (Cd) and Lead (Pb). The total concentration of metals in sediments were ranged from 43.78 to 82.38 µg/g for Cr, from 300.32 to 1237.32 µg/g for Mn, from 18.51 to 40.91 µg/g for Ni, from 27.34 to 116.46 µg/g for Cu, from 129.98 to 832.64 µg/g for Zn, from 5.58 to 19.62 µg/g for As, from 0.62 to 3.29 µg/g for Cd and from 40.42 to 83.52 µg/g for Pb respectively. The metals concentration was spatially varied in this Lagoon and maximum concentrations were observed in the upstream lakes (S3) and downstream of the outlet channel (S18). Therefore, minimum metals concentrations were found mostly in the inlet channel (S13, S14) of the Lagoon. In comparison with the marine sediment quality (GB18668-2002, China), it has demonstrated that average concentrations of Cd, Pb, Zn and Cu were higher than class I level of sediment marine quality. And, maximum concentration of Cd, Zn and Cu (Upstream lakes and downstream sampling areas) were higher than class II marine sediment quality level. In addition, maximum concentrations of all metals were higher than the world average shale concentration. The Geo-accumulation indices of Cr, Mn, Ni and As indicate no contamination of these metals, but Cu, Zn, Cd and Pb showed moderate to high contamination levels. Overall, the mixture of metals contamination degree (C_d) indicates all the metals were moderate to considerable degree pollution of this Lagoon. The potential ecological risk (E^r_i) showed a low potential risk for Cr, Mn, Ni, Cu, Zn, As, and Pb in all sampling areas and Cd showed low to considerable ecological risk in the studied areas. Pearson correlation and principal component analysis suggest that Zn, Cu, Cd, Pb TOC were originated from the same anthropogenic sources. Strom water, industrial discharge, domestic sewerage, runoff, combustion of gasoline, boat riding were the important sources to import heavy metals in the Yundang lagoon. Overall, to reduce to pollution level, remediation strategy should be implemented according to the contamination level of different areas.