The deteriorating water quality (WQ) of the sacred north-flowing perennial Indian River, Ganga was a serious concern in recent decades for population adjoining to the river and policy planners. The present evaluation attempts to assess the long-term (1989–2016) physiochemical characteristics of WQ of river Ganga at five upstream locations (Uttarkashi, Tehri, Rudraprayag, Devprayag, and Rishikesh) of Uttarakhand, India using comprehensive pollution index (CPI) and environmetrics (PCA and CA). These methods were used to categorize, summarize expensive datasets, and grouping the similar polluted areas along the river stretches. The WQ of river at all the locations were within the good category and most of the physiochemical parameters were well within their acceptable limit for drinking WQ. Considerably, CPI demonstrated the river WQ was in slight pollution range (CPI: 0.40–1.00) in the year 2007 and 2015 at all the five locations. The positive correlation coefficient (R
2
> 0.50) among NO
2
NO
3
, Ca, Na, B, and K indicates the significant contribution of organic and inorganic salts through runoffs from catchments due to weathering of rocks. PCA confirmed the input source of nutrients in the river from both natural and anthropogenic sources. Moreover, the upstream WQ assessed was found to be good as compared to the severely polluted downstream region. Due to COVID-19 and shutdown in the country, reduction of pollution load in the river was observed due to the rejuvenation capability of river Ganga. This information can assist the environmentalist, policymaker, and water resources planners & managers to prepare strategic planning in advance to maintain the aesthetic and cultural value of Ganga river in future.