Water quality plays a vital and key role in estimating the diversity and abundance of phytoplankton in freshwater ecosystem. The water quality of freshwater body is rapidly deteriorating by various anthropogenic activities and diverse emancipations from the population growth, urbanization, and industrialization. The aim of present research work was to estimate the anthropogenic influence on water quality and phytoplankton diversity of upper Ganga basin. The water quality and plankton diversity of a Ganga River and its major tributaries was studied between September 2018 and September 2020 in eight sampling stations. Some physico‐chemical parameters like turbidity, dissolved oxygen, and biological oxygen demand showed a slight increase in sampling stations 7 and 8. Multi‐correlation was calculated between physico‐chemical parameters and phytoplankton density. Totally 31 genera of phytoplankton were recorded and represented by five groups, Bacillariophyceae (14 genera), Chlorophyceae (11 genera) Myxophyceae (4 genera), Euglenophyceae (1 genera), and Xanthophyceae (1 genera). Dissolved oxygen showed a direct influence on the distribution of plankton and also showed a positive correlation with phytoplankton diversity. Finally, it can be concluded that human activities including River bed mining, construction of Dam, and barrages had negatively impacted the water quality and phytoplankton diversity. Still, these kinds of activities to be checked regularly and can be controlled.