The occurrence, abundance, and distribution of phytoplankton have been investigated upstream and downstream of three barrages on the river Ganga at Bijnor, Narora, and Kanpur in Uttar Pradesh, India. A total of 104 phytoplankton species belonging to eight phyla (Bacillariophyta, Charophyta, Chlorophyta, Cryptophyta, Cyanophyta, Euglenophyta, Miozoa, and Ochrophyta) were identified during the sampling period. During the summer, monsoon, and post-monsoon seasons, the density of phytoplankton (Ind. L⁻¹) ranged from 9.6 × 10⁴ to 2.03 × 10⁷, 9.6 × 10⁴ to 4.5 × 10⁵, and 2.2 × 10⁵ to 2.17 × 10⁶, respectively. The species abundance and the relative abundance showed an increasing trend from the first (Bijnor) to the third (Kanpur) barrage, suggesting a gradual decrease in river flow and an increase in residence time. Phytoplankton cell density in Kanpur, however, was unexpectedly higher and showed eutrophic conditions attributable to elevated organic load and surplus nutrients from the land runoff. One-way ANOVA (post-hoc Tukey test) showed statistically significant (p < 0.05) seasonal variation in temperature, transparency, free CO2, PO4³⁻, and dissolved organic matter. Analysis of Pearson’s correlation coefficient suggested a statistically significant correlation (p < 0.05) of mostly phytoplanktonic groups with free CO2, CO3²⁻, HCO3⁻, Cl⁻, specific conductivity, total dissolved solids, total hardness, Mg²⁺, PO4³⁻, and SiO4⁴⁻. The minimum species diversity was recorded during the monsoon season, while the maximum diversity was reported during the post-monsoon season which might be due to high nutrient load and a high concentration of PO4³⁻ post-monsoon. We concluded that aquatic biodiversity and ecological structure could be adversely influenced by a series of obstructed barrages and dams, which influenced the assemblage pattern of phytoplankton communities.