Human activities, including industrialization, population growth, and the extensive use of fertilizers, chemicals, and effluents, have resulted in contamination of natural water sources. This study presents a comprehensive assessment of the Bhagirathi River for the Water Quality Index (WQI), focusing on the temporal variations in physico-chemical characteristics between 2015 and 2020. Utilizing remote sensing (RS) for efficient data collection and geographic information system (GIS) for spatial and temporal analysis, the study identifies ecological and socio-economic impacts along the river’s course. The research highlights the critical role of atmospheric adjustments in satellite-based water quality assessments. Analysis of water samples from Uttarkashi to Rishikesh reveals a slightly alkaline pH, with an increase in conductivity, turbidity, and total solids. Seasonal variations show high dissolved oxygen levels, low biochemical oxygen demand (BOD), and chemical oxygen demand (COD) during the monsoon season. Ion concentrations, including sodium, potassium, calcium, magnesium, chloride, sulfate, and iron, were found to be within acceptable limits, with no detectable heavy metals. Comparisons with WHO standards indicate that the quality of water of the Bhagirathi River remains generally good in condition, requiring minimal treatment, except in specific regions such as Uttarkashi, Tehri, and Rishikesh during the monsoon season. Despite contamination from flooding, high precipitation, and human activities, the water is deemed safe for agricultural as well as industrial use. This study underscores the importance of continuous monitoring and targeted interventions to maintain the quality of water in the Bhagirathi River.