Benthic diatoms are important primary producers in river ecosystems and serve as sensitive indicators of nutrient dynamics and ecological health. To elucidate the spatiotemporal distribution patterns of benthic diatom communities and their responses to environmental factors in the mainstream of the Fenhe River, seasonal surveys were conducted at 25 sampling sites along the mainstream during four seasons from April 2021 to January 2022. Community composition, diversity, and relationships with physicochemical variables were systematically investigated. The results indicated pronounced seasonal and spatial variations in benthic diatom communities. Diatoma moniliformis dominated in spring, autumn, and winter, whereas the abundance of Cyclotella meneghiniana increased markedly in summer. Although α-diversity indices showed no significant overall differences among seasons, clear spatial patterns were observed, with significantly higher values in the upstream reaches than in the middle and downstream reaches. β-diversity analyses demonstrated that both season (R2 = 0.143, P = 0.001) and river reach (R2 = 0.136, P = 0.001) exerted significant effects on community structure. Redundancy analysis (RDA) further revealed that water temperature, pH, dissolved oxygen, total dissolved solids, and total phosphorus were the principal environmental factors driving the distribution of benthic diatom communities.