To elucidate relationships between phytoplankton and related environmental factors, phytoplankton and environmental parameters of water quality in the Daning River were conducted using multivariate statistical analysis. Most of the investigated physico chemical parameters [water temperature, total nitrogen, nitrate-N (NO3(-) -N), pH and dissolved oxygen concentration (DO)] in Daning River are significantly different among those sampling sites (ANOVA, p < 0.05). The results indicate that the Daning River has a comparatively high spatial and temporal heterogeneity in the phytoplankton community composition (ANOVA, p < 0.05). The maximum cell density was recorded in Dachang and the minimum density was found at Wuxia-kou sites. Multi-algal species blooms were observed in the same time and place with the maximum density appeared. Correlation analysis was performed to illuminate the relationships between algae density and environmental variables, TN (r = - 0.789, p < 0.05), NO3(-) -N (r = - 0.825, p < 0.05) and NO2(-) -N (r = -0.803, p < 0.05) were negatively correlated with algae density. The results indicate that nitrogen soluble nutrients are key regulatory factors for phytoplankton abundance. The results of redundancy analysis (RDA) indicate that main soluble nutrients (TN, TP, NO3(-)-N and NO2(-)-N), suspended substance (SS) and transparency contributed significantly to phytoplankton community composition. Phytoplankton growth could enhance the pH value. The environmental characterizations and sample sites adjacency contributed significantly to phytoplankton community composition.