Abstract Surveys of zooplankter and phytoplankton through environmental DNA (eDNA) and metagenomic technology across Dianchi Lake and the estuary of inflowing rivers was conducted, to evaluate the microbial diversity of Dianchi Lake and the estuary of four in flowing rivers. Diversity of plankton and the similarity of dominant species results revealed that the dominant eukaryotic phytoplankton in Dianchi Lake was Bacillatiophyta. The Shannon diversity index values of phytoplankton and zooplankton ranged from 3.68 to 18.36 and 0.54 to 2.49, respectively. The main genus taxa in the Dianchi Lake were similar with the inflowing river. The distribution map of Shannon diversity index gave overall insight into the variation of plankton diversity. The research proved that the eDNA technology was effective in biodiversity monitoring in aquatic ecosystem, and the inflowing river may impose an adverse influence on the ecosystem health of Dianchi Lake.