Metal-contaminated sediments in lakes is a global concern that poses toxicological risk to aquatic organisms. This study performed bioassays using the submerged macrophyte, Vallisneria natans (Lour.) Hara, exposed to contaminated sediments collected from five locations in Dianchi Lake, Yunnan, China. Among the sediments collected, Igeo showed enrichment of As and Cd in Dianchi Lake sediments. In spite of enriched toxic metals at some locations, laboratory bioassays found no significant difference in leaf biomass or leaf photosynthesis rate between the sites. Root biomass and root activity showed significant differences between locations and were negatively correlated with the concentration of As, Cd, Hg, and Pb in sediment but not related to Cr. The above correlations were strongest for Hg and As, respectively. Accumulation of Cd and Pb to leaves of bioassay plants was observed, but this was not evident for As and Cr. Overall, the results indicate that V. natans can be used as a bioassay organism and measures of root toxicity are sensitive to metal concentrations present in Dianchi Lake sediments. Furthermore, the study species holds promise for use as a biomonitor of Cd and Pb sediment metal content.