Shengjin Lake is a typical Yangtze River-connected lake, that is also a national nature reserve and a Wetland of International Importance. In order to evaluate the eco-environmental evolution of Shengjin Lake, a²¹⁰Pb- and ¹³⁷Cs-dated sediment core collected from the upper part of the lake was analyzed. Based on a biological indicator (subfossil cladoceran) and geochemical indicators (loss on ignition (LOI), total organic carbon (TOC), δ¹³C of bulk sediments (δ¹³C_org), total phosphorous (TP) and total nitrogen (TN)), we revealed the changes in the cladoceran assemblages and eco-environmental processes of Shengjin Lake. The results showed that there was a healthy ecological environment with low nutrient levels in Shengjin Lake before the 1980s. However, the increasing levels of the eutrophic species B. longirostris, nutrients (TN and TP) and organic matters (LOI and TOC), and the decreasing δ¹³C_org in recent decades indicated that the trophic state of Shengjin Lake has increased since the 1980s. This corresponded with increasing anthropogenic effects, including land reclamation, chemical fertilizer application, and sluice construction. In addition, the droppings of water birds also promoted increases in nutrient and organic matters levels in Shengjin Lake.