Accumulation of trace metals in sediment can cause severe ecological impacts. The present study determines the elemental concentrations and chemical partitioning of heavy metals in surface sediment of Shadegan wetland. Shadegan wetland is one of the most important wetlands in southwest of Iran and it is in Ramsar-listed wetlands. For this purpose, 7 sampling stations were selected for sediment collection in this wetland during autumn 2011. Physico-chemical parameters including pH, EC, total organic materials (TOM), grain size fraction and elements (Cr, Pb, V,) in sediments were measured. Subsequently, lithogenous and anthropogenic portions of trace metals in sediment, along with Igeo and IPOLL indices were measured. According to obtained results, Pb(25%), and Cr (14 %), had highest anthropogenic portion in study area. More ever, strong and positive meaningful relation between Cr and V shows that Cr has oil origin in the area of the study. Also, measured physico-chemical parameters have no role in controlling the trace elements concentration. The two pollution indices used in the present investigation (Igeo and IPOLL) are indicative of different pollution intensity in Shadegan aquatic environment.