Historical legacy effects and the mechanisms underlying primary producer community succession are not well understood. In this study, environmental DNA (eDNA) sequencing technology and chronological sequence analysis in sediments were utilized to examine long-term changes in cyanobacterial and aquatic plant communities. The analysis results indicate that the nutritional status and productivity of aquatic ecosystems have been relatively high since 2010, which could reflect a period of eutrophication due to high long-term rates of organic matter deposition (33.22–42.08 g·kg⁻¹). The temporal and spatial characteristics of community structure were related to environmental filtering based on trophic status between 1849 and 2020. Turnover in the primary producer community was confirmed through change-point model analyses with regime shifts toward new ecological states. On the basis of ecological data and geochronological techniques, it was determined that the quality of habitats at a local scale may affect ecological niche shifts between cyanobacterial and aquatic plant communities. These observations suggest how primary producers respond to rapid urbanization, serving as an invaluable guide for protecting freshwater biodiversity.