Introduction: Phytoplankton which can affect higher trophic levels play a pivotal role as primary producers. Phytoplankton structure and diversity may, besides other factors, be controlled by the changing of water temperatures. Hence, the present study aimed to determine some relationship between phytoplankton assemblage and water temperature in Ba Lai River, Vietnam. Methods: In this research, sample data along the Ba Lai Estuary during two surveys were carried out in rainy season (September, 2017) and in dry season (March, 2018), and analyzed by Spearman's correlation and Linear regression analysis to find the correlations. Results: The results showed that the temperature of surface water in Ba Lai River was quite stable spatially. A total of 128 species belonging to 5 groups- namely cyanobacteria, diatoms, green algae, euglenids and dinoflagellates- were recorded in which diatoms were clearly dominant. Additionally, multiple stepwise linear regression revealed that phytoplankton assemblage correlated significantly with the temperature of surface water. The water temperature had a significant positive correlation with chlorophyll-a concentration but was negatively correlated with Margalef's diversity index in the rainy season. Moreover, the significant negative association of water temperature with biomass of phytoplankton and biomass of diatoms, which was principal in species number, were determined in the dry season. Conclusion: This study investigated the phytoplankton communities and found their correlation with environment in the area, and demonstrated advantages of phytoplankton which warrant their further research.