The growth and development of phytoplankton are influenced by physico-chemical parameters, which can also affect the spatial distribution of phytoplankton community structure. However, it is unclear whether environmental heterogeneity caused by multiple physico-chemical factors can affect the spatial distribution of phytoplankton and its functional groups. In this study, we investigated the seasonal variation and spatial distribution of phytoplankton community structure and its relationships with environmental factors in Lake Chaohu from August 2020 to July 2021. We recorded a total of 190 species from 8 phyla, which were divided into 30 functional groups, including 13 dominating functional groups. The average annual phytoplankton density and biomass were (5.46 ± 7.17) × 107cells/L and 4.80 ± 4.61 mg/L, respectively. The density and biomass of phytoplankton were higher in summer ((14.64 ± 20.34) × 107cells/L, 10.61 ± 13.16 mg/L) and autumn ((6.79 ± 3.97) × 107cells/L, 5.57 ± 2.40 mg/L), with the M and H2 of dominant functional groups. The dominant functional groups were N, C, D, J, MP, H2, and M in spring, whereas functional groups C, N, T, and Y dominated in winter. The distribution of phytoplankton community structure and dominant functional groups exhibited significant spatial heterogeneity in the lake, which was consistent with the environmental heterogeneity of the lake and could be classified into four locations. Location I had higher phytoplankton density and biomass than the other three locations. Additionally, dominant functional groups M, C, and H2 were present throughout the lake, and all 13 dominant functional groups were observed in Location II. Our findings suggest that environmental heterogeneity is a key factor influencing the spatial distribution of phytoplankton functional groups in Lake Chaohu.Supplementary InformationThe online version contains supplementary material available at 10.1007/s11356-023-28043-5.