Dongting Lake is one of the most important inland freshwater lakes in China. To investigate the spatial distribution and seasonal variation characteristics of heavy metals (Cr, Co, Cu, Zn, Cd, and Pb) in the lake, 53 surface sediment samples were collected in the East Dongting Lake (ED Lake) in the wet and dry seasons. Results show Cr, Co, Cu, Zn, Cd, and Pb contents were 1.7 (1.9), 1.8 (2.0), 2.9 (3.0), 1.9 (1.9), 11.7 (13.1), and 2.0 (2.2)-fold of their geochemical soil background values of Hunan province (China) in the wet (dry) season. Spatial and seasonal heterogeneity could be found in the distribution of Cr, Co, Cu, Zn, and Pb in the surface sediments. The enrichment factor (EF) suggested that Cd has reached severe enrichment in the sediment. The result of the geo-accumulation index ($${I}_{geo}$$
I
geo
) indicated that Cr, Co, Cu, Zn, and Pb were at levels corresponding to low contamination, and moderately to highly polluted with Cd. Multivariate statistical analysis including pearson correlation analysis and principal component analysis was used for the identification of potential sources of the heavy metals in the sediments. The results showed that Cu, Zn, and Pb from the sediments of the East Dongting Lake in the wet and dry seasons were possibly anthropogenic sources, such as emissions from mining and smelting while Al, Fe, and Cr are attributed for natural sources. Cd enrichment in the sediments is influenced by both natural factors, and human activities in local areas.