Phytoplankton diversity and community characteristics are closely associated with aquatic environmental factors. Understanding these dynamics can provide insights into the ecological health of water bodies. We investigate the spatial and temporal characteristics of phytoplankton communities in 27 drinking water source reservoirs in Shenzhen, China. As a method, we collected samples during the dry season in 2021 and the wet season in 2022, analyzed the alpha and beta diversities of phytoplankton communities, and correlated these with the environmental factors. The results reveal that Cyanobacteria dominate the phytoplankton communities in the Shenzhen reservoirs. Phytoplankton diversity is greater during the dry season. The algal composition varies spatially, and the phytoplankton diversity tends to decrease with increasing eutrophication. A co-occurrence network analysis indicates denser and stronger correlations among phytoplankton nodes during the wet season than dry season. Reservoirs with moderate eutrophication levels exhibit denser nodes and stronger correlations compared to those with low or high eutrophication levels. The chemical oxygen demand, water temperature, pH, and total nitrogen are identified as key influencers of the phytoplankton community structure. Our results contribute to the enhanced understanding of the spatial and temporal dynamics of phytoplankton communities in reservoirs in South China and provides insights into the management and conservation of these drinking water reservoirs.