This study discusses changes in connected water systems in Chagan Lake induced by the interference of natural and human activities, based on the analysis of sediment characteristics. In this study, the following sediment characteristics were investigated in the lake area, the natural supply area, and the lake drainage area: mineral composition; particle size distribution; magnetic susceptibility; nutrient content; content of isotopes δC and δN; and content of heavy metals and of metallic oxides. The results showed that silicate minerals quartz, orthoclase, and anorthose were abundant in the whole lake water system. Quartz accumulated more easily in the lake area, while carbonate masses in the lake mainly came from the Huolinhe River. Moving from the lake area to the water diversion and drainage areas, fine particles clearly decreased, while coarse particles significantly increased due to the increase in hydraulic erosion. The main sources of nutrients and of organic matter are: the residual of the drainage from the Qianguo irrigated areas; the surrounding villages and the tourist area; and the decomposition of aquatic organisms. A large number of anthropogenic heavy metals, such as Hg, Cu, and As, were accumulated in the artificial water diversion area and in the farmland drainage area. This study indicates that recovering the original connected water system during the wet season, while at the same time enhancing water supply during the dry season could improve the ecological quality of Chagan Lake.