© 2022 Elsevier B.V.Diverse aquatic macrophyte communities represent an essential component of healthy shallow lake ecosystems, and information on changes in macrophytes abundance and composition is crucial for restoration initiatives and management. However, the long-term dynamics of aquatic macrophyte communities are poorly understood for most subtropical freshwater lakes. This study used macrophyte surveys from 1960 to 2014 alongside plant macrofossil and pollen remains deposited in the sediment to reconstruct, macrophyte community change over the two centuries in the southeastern bay of Lake Taihu, China. Plant macrofossils efficiently captured the main historical recorded macrophyte species, including four unrecorded submerged taxa (Vallisneria spinulosa, Zannichellia palustris, Nitella sp., and Chara sp.) by the monitoring surveys. Aquatic pollen failed to reflect the main species composition in the bay, but provided additional information on species with no macrofossils and few seeds, especially the floating-leaved and free-floating taxa (e.g., Nymphoides and Azolla). We conducted a constrained incremental sum of squares cluster analysis and a multiple factor analysis (MFA) to the macrophyte community in the core and identified three major changes over the past century, with a shift from Potamogeton malaianus (pre-1960), to Vallisneria natans, P. malaianus, Potamogeton maackianus, and charophyte species (1960–1998), followed by the proliferation of pollutant-resistant species Ceratophyllum demersum and Myriophyllum spicatum, as well as the floating-leaved plant Nymphoides (post-1998). MFA also clearly elucidated the relationships between macrophyte shifts and changes in various environmental stressors (i.e., cladocerans, particle size spectra and geochemical data). The results confirmed our hypothesis, which stated that hydrological alterations and increased nutrient inputs, driven by the increasing anthropogenic pressures were likely the main drivers of the alteration in the macrophyte composition and succession in the bay. Our study provides a unique perspective on the pre-disturbance macrophyte community composition of Eastern Lake Taihu, thereby offering useful information not only for lake managers in the Yangtze region, but also for the global decision-making for the eutrophication and restoration of large shallow lakes.