Understanding the temporal and spatial dynamics of phytoplankton is crucial for assessing water quality in freshwater ecosystems. In this study, the temporal and spatial distribution of phytoplankton and its correlation with environmental factors were studied during the Summer and Autumn of 2022 in the Nanjiang Reservoir, China, to determine its water quality. Water sampling was conducted monthly for 5 months at four fixed sites along the reservoir. Phytoplankton species composition and abundance were analysed based on the Utermöhl method while the physico-chemical parameters were analysed based on standard methods. The study identified 198 species, 74 genera, and 7 phyla (Bacillariophyta, Chlorophyta, Cyanophyta, Euglenophyta, Dinophyta, Cryptophyta, and Chrysophyta) in the reservoir. Bacillariophyta displayed the greatest cellular abundance and species diversity during the study period. The average abundance of phytoplankton in summer (217.76 ± 13.59 × 104 cells/L) was higher than that in autumn (178.93 ± 13.59) × 104 cells/L). The upstream of the reservoir represented the highest phytoplankton density, biomass, and diversity attributable to the highest concentrations of nutrients from the river's influx observed in the same section. Correlation and Redundancy analysis (RDA) highlighted water temperature, pH, and Total Dissolve Solid (TDS) as the most important environmental factors influencing phytoplankton community structure. These findings highlight the importance of monitoring phytoplankton dynamics as a reliable indicator of water quality in reservoirs and may have implications for Nanjiang Reservoir management and conservation efforts.