The region has been increasingly experiencing environmental issues related to heavy metals (HMs) due to human activities. However, the contamination levels of HMs (Cr, Ni, Cu, Zn, As, Cd, and Pb) in various inner lakes in the Dongting Lake area remain unclear. In this study, surface sediment samples from 9 inner lakes and sediment core samples from 3 typical inner lakes were collected to evaluate the spatial distribution, contamination status, environmental and ecological risks, and possible sources of these HMs. The results showed that all HMs, except Zn, exceeded background values, with particularly high levels observed in aquaculture lakes compared to other lakes. Vertical profiles of HMs from 3 lakes show that the various types of lakes in the study area have different pollution histories. Additionally, results from Sediment quality guidelines (SQGs), Contamination factor (CF), Geo-accumulation index method (Igeo), and Hakanson potential ecological risk index (PERI) indicated that As, Cd, and Pb are the primary pollutants. The multivariate analysis concluded that Ni, Cu, Zn, As, Cd, and Pb had anthropogenic sources, primarily from agricultural, fisheries, industrial, and transportation activities, while Cr was influenced by natural factors. The results of this study enhance our understanding of sedimentary metal content in inner lakes and emphasize the importance of controlling HMs content in these lakes. This information is crucial for developing effective lake management and pollution control strategies.