Heavy metal (HM) contamination has become a widespread global problem and posed threat to the aquatic environment due to their toxicity, persistence and bioenrichment in the food chain. In this study, overlying water, sediment, Potamogeton pectinatus L. (P. pectinatus), Phragmites australis (P. australis), and four types of fish in Wuliangsuhai Lake, China, were analyzed for HMs. The Inductively Coupled Plasma Mass Spectrometry (ICP-MS) was used to determine the contents of HMs in collected samples in order to investigate their spatial distribution, enrichment characteristic, risk assessment and the possible sources. The results showed that: (1) The mean levels of Cr, Ni, Cu, Mn, Pb and Zn mainly followed an order of sediment>P. pectinatus (submerged plants)>P. australis (emergent plants)>fishes>overlying water, but for As, the concentration in overlying water was higher than that in P. australis and fishes. The content of Cd, in P. australis was almost 50 times higher than that in normal plants and in fish was 3.3 times higher than the permissible threshold standards in China, leading to potential hazards to fish and human health via food chain bioaccumulation. (2) In sediment As and Cd experienced moderately severe enrichment. For P. pectinatus, the higher bioconcentration factor (BCF) and the lower biota-sediment accumulation factor (BASF) indicated that this species was more likely to accumulate HMs from overlying water and could remove HMs from Wuliangsuhai Lake as a hyperaccumulator. (3) In sediment, the Eri and RI values suggested that Cd posed a considerable high ecological risk and a very high risk to the surroundings. Because of the high HM contamination levels in the northwest part of the lake, the inlet and outlet of the lake were identified as priority regions for metal pollution monitoring and management. (4) The results of source identification indicated that Zn and Cd were derived from mining and industrial wastewater, while As was related to nonpoint source pollution from agriculture. These results will provide important information for improving the aquatic environment, minimizing the potential risks posed by the HMs pollution in Wuliangsuhai Lake and managing the water quality of the Yellow River.