This study takes the west side of Lake Bosten as the study area. In this study, the distribution characteristics and influence factors of heavy metals in different media were discussed. Carrying out this study played an important role in expanding the research of heavy metals in arid regions lake environmental geochemistry process. The results revealed that the heavy metals concentrations of water bodies in all areas, except for Cd, were lower than the threshold of class I regulated in the Environmental Quality Standards for Surface Water in China. The heavy metals in sediment were still at low risk level, but the Cr and Ni in the sediments showed a remarkable growth trend in recent year. Therefore, the potential ecological risk should not be ignored. Zn, Pb and Ni are mainly accumulated in the root of the reed, and the distribution of Pb was the most prominent. However Cd and Cu are mainly accumulated in stem, and the concentrations of Cr in each tissue is relatively uniform. Ni and Pd spatial distribution in sediments and water are accordance, but different in reed. Nevertheless, the Cu, Cd and Pb distributions among the three sampling sites are different. This is mainly because of the diverse ways of absorbing heavy metals in different media and the different pollution history in different sampling points. In the western of the lake Bosten, the heavy metal distributions among the three compartments were significantly different, with the following order: sediment > plant > water.