Dawangtan Reservoir is a typical large drinking water source reservoir in the south subtropical region. Cyanobacterial dominance and algal blooms caused by eutrophication pose major threats to its water supply security. Understanding the characteristics of the phytoplankton community and the driving factors behind cyanobacterial dominance is of great significance for algal bloom prevention and the management of reservoir water supply safety. A quarterly investigation of the aquatic environment and phytoplankton community in the Dawanqtan Reservoir was conducted in 2021 to explore the seasonal dynamics of the phytoplankton community and the driving factors behind the dominance of filamentous cyanobacteria. The results indicated that the phytoplankton in Dawangtan Reservoir comprised 127 species from 7 phyla, with Chlorophyta, Bacillariophyta, and Cyanophyta being the dominant groups in terms of species composition, belonging to 26 functional groups. The phytoplankton cell density ranged from 1.2×106 to 430×106 cells/L, exhibiting the order of autumn ＞ spring ＞ winter ＞ summer, while the biomass ranged from 0.14 to 51 mg/L, with the order of autumn ＞ winter and spring ＞ summer. The dominant genera wereLimnothrix andPseudanabaena, and the functional group S1 was the long-term dominant functional group. The comprehensive trophic level index (TLI) of the reservoir ranged between 36.02 and 49.57, indicating a mesotrophic state. Mantel tests and redundancy analysis (RDA) revealed that water temperature, transparency, and nitrogen concentration were significant explanatory variables influencing the dominance of filamentous cyanobacteria. The absolute dominance of filamentous cyanobacteria occurred in Autumn, characterized by lower transparency and nitrogen concentration but higher water temperature, representing a high-risk period for blooms ofLimnothrix andPseudanabaena. Combined with functional group analysis, the results indicate that the turbid environment of large reservoirs is an important factor promoting the dominance of filamentous cyanobacteria. In Autumn, water temperature and nutrient conditions fall within the optimal range for the growth ofLimnothrix andPseudanabaena, serving as key drivers for their massive proliferation. Given the threat posed by filamentous cyanobacteria such asLimnothrix andPseudanabaena, attention should be paid to the causes of increased turbidity and water color in reservoirs to improve water transparency and thereby limit the formation of filamentous cyanobacterial dominance.