Submersed macrophytes are an integral component of shallow lake ecosystems, and their distribution patterns are influenced by environmental factors, particularly water depth. Key factors affecting the growth of submersed macrophyte vary across different water depth gradients, and they interact synergistically with water depth conditions to influence submersed macrophyte communities. Dongshan Bay, a typical macrophyte-dominated lake area in the eastern part of Lake Taihu, was selected as research area in this study. From October 2020 to June 2021, three surveys were conducted on water physicochemical indicators and the species richness and abundance of submersed macrophyte at 31 sampling sites with varying water depths. The relationship between submersed macrophyte and environmental factors at different water depths were analysed using one-way ANOVA, Spearman correlation analysis, and redundancy analysis, to identify key environmental factors influencing submersed plant community composition in different water depth zones. The results indicated: 1) physicochemical parameters of the water exhibited significant spatiotemporal differences. The average chlorophyll-a (Chl.a) content and the ratio of Secchi depth to water depth (SD/WD) in the nearshore waters of shallow areas in the Dongshan Bay of Lake Taihu were significantly higher than those in deeper near-lake center area. Total nitrogen (TN), nitrate nitrogen, total phosphorus (TP), phosphate and suspended solids concentrations were significantly higher in spring than in autumn and summer. 2) This study recorded 12 species of submersed macrophyte in Dongshan Bay, with higher frequency of submersed macrophyte in the middle waters. The submersed macrophyte communities in different water depth areas showed differences in species composition, with species like Potamogeton wrightii/Potamogenton malaianus, Vallisneria natans and Hydrilla verticillata exhibiting higher frequency and abundance in the near-lake center area. 3) Key water environmental factors influencing the submersed macrophyte community in the Dongshan Bay include water depth, TN, TP, SD/WD and Chl.a, and the composition of submersed macrophyte communities in different water depth areas is regulated by different water environmental factors. The key environmental factors affecting submersed macrophyte growth in shallow nearshore areas include water depth and Chl.a; submersed macrophytes in the midwater area are mainly influenced by water TN and TP; while submerged macrophytes in deeper areas near the lake center are significantly correlated with water depth, TN and TP. The results of this study provide important theoretical basis for shallow lake water level management and submersed macrophyte restoration under different water depth environments.