Concentrations of cadmium (Cd), lead (Pb) and arsenic (As) in submerged macrophytes, the corresponding sediments and water (surface water, pore water and overlying water) of Lake Baiyangdian have been determined to investigate the pollution and distribution characteristics of heavy metals in sediment-submerged macrophyte-water system and heavy metals accumulation ability of submerged macrophytes. The results showed that Cd, Pb and As concentrations in surface water meet the standard of Class I of Environment Quality Standards for surface water (GB 3838-2002), and no significant difference was observed in heavy metals concentrations between different regions. Pb concentrations in overlying water is greater than that in surface and pore water, while As concentrations in pore water is significantly higher than that in surface and overlying water. In addition, results of geo-accumulation index (I_geo) and potential ecological risk index (RI) showed that, heavy metals pollution in sediment in the pattern Cd > Pb > As, with Cd coming up to slight to partial severe pollution and media to extremely strong ecological risk while As is still clean. Further, heavy metals contamination in sediment of different areas decreased in the order of Living and aquaculture area > Sewage residence area > Fringe area. Among the samples of submerged macrophytes the concentration of heavy metals were decreased in the order of Ceratophyllum demersum > Potamogeton crispus, Myriophyllum spicatum > Potamogeton pecinatus. It is worth noting that heavy metals concentrations in submerged macrophyte display obvious positive correlations with nitrogen and phosphorus concentrations in plants, which means that nitrogen and phosphorus may enhance heavy metals accumulation of submerged plants.