To elucidate the spatial distribution characteristics of algal communities and their correlation with environmental factors in the Heilongjiang River, algal surveys and water quality monitoring were carried out from May to October 2023. The results were as follows: (1) In total, 234 species from 95 genera belonging to seven phyla were detected, mainly Bacillariophyta, Chlorophyta, and Cyanophyta. (2) The most dominant species in the Heilongjiang River in summer and autumn were Pseudanabaena minima (G. S. An) Anagnostidis and Phormidium gelatinosum Woronichin. The dominant species in the middle niche in summer and the dominant species in the broad niche in autumn were Bacillariophyta. (3) Canonical Correlation Analysis results revealed that the environmental factors that significantly affected the distribution of the epiphytic algae during the summer were COD, F-, and WT, while EC, TN, BOD₅, and pH significantly influenced the distribution of epiphytic algae in autumn. (4) Significant correlation heatmaps revealed that the dominant species were significantly correlated with WT and TP in the Greater Khingan Mountains in summer, whereas the dominant species were significantly correlated with COD, NH₃-N, and TP in the Heihe region, Lesser Khingan Mountains, and Sanjiang Plain. There was a significant correlation between the dominant species and TN in the Greater Khingan Mountains in autumn. The spatial distribution characteristics of the algal communities and the correlations between the dominant species and water environmental factors can provide a theoretical reference for the assessment of the water ecological health status.