An overall and comparative ecological risk assessment of heavy metal pollution (including Cu, Zn, Pb, Cd, Hg, Cr, As, and Ni) in surface sediments was conducted for six major shallow freshwater lakes (Taihu Lake, Chaohu Lake, Nansihu Lake, Dongting Lake, Poyang Lake, and Hongze Lake) in China. A spatial database with 339 sediment samples was created through an extensive literature survey. Consensus-based sediment quality guidelines (SQGs) were used as the effect thresholds due to the lack of local eco-toxicological information about heavy metals in the six lakes. The results show that the ecological risk of heavy metal pollution in surface sediments is highest in Dongting Lake, followed by Taihu Lake. Lakes Chaohu, Nansihu, Poyang, and Hongze are at a similar risk level, which is a little lower than that of Lake Taihu. High-risk areas that should be given more attention were identified by spatial analysis. The estuaries of the inlets and outlets of Dongting Lake and the Meiliang Bay in Taihu Lake were found to be such areas. Ineffective environmental supervision and management during the recent years of rapid economic and industrial development in China have led to the pollution of lake sediments by heavy metals. Rigid control and effective management measures to prevent heavy metal pollution are urgently needed in China. In addition, it is necessary for China to develop basic research on the local eco-toxicity and SQGs of freshwater sediments to provide a scientific basis for the management of lake sediment pollution.