Periphytic algal assemblages in the River Sindh of Kashmir Himalaya were studied in relation to environmental factors and anthropogenic alterations like flow regulation for Run-of-River hydropower plants to understand their ecology in a regulated river ecosystem. Sites were sampled from unregulated, regulated, and downstream reaches along the river on a seasonal basis from the year 2017 to 2019. A total of 48 species were identified, spread over 31 genera. Non-metric multidimensional analysis showed clear distinction in periphytic algal assemblage samples based on sites and potentially some more minor distinction based on seasons rendering the sites into two distinct groups (G1 and G2). The ADONIS test showed that the groups (G1 and G2 sites) do not significantly differ in terms of how communities differ from one another, but there is a difference in species compositions based on seasons. However, the betadisper test indicated that groups (G1 and G2 sites) and seasons present homogeneity among group dispersions (compositions vary similarly) while having significantly different compositions. Geo-physical factors (discharge and altitude) accounted for most variations, while the scraper community played a minor role. This study provides scientific insights related to the ecology of a regulated Himalayan river and may provide information relevant to managing the River Sindh sustainably.