National river of India, Ganga River, nurturing ecological, economic, and socio-cultural aspects defining the last long history of country. Forming the largest catchment, fulfil the needs of millions of people for fresh water used in domestic, agriculture, commercial and industrial sectors. Therefore, River Ganga is always the center of attraction to the administrative authorities, institutions, academicians and researchers for its quality issues. The periodically examination of the river water quality for its conservation, restoration or rejuvenation is essential and conducted by many researcher on different quality aspects. The aim of the present investigation is to estimates the spatio-temporal variability in the Ganga River System's hydrology in upstream regions in the Himalayan Region of Uttarakhand state, India. The result clearly explains considerable variation in water quality index (WQI: 29.39–71.60) screening seasonal variation, defining the deterioration of water quality (WQ) of Ganga River from good to moderate polluted level through the overall index of pollution (OIP). Moreover, principal component analysis (PCA) has implied to identify the pollution sources. The PCA generates seven components and contributes (85.1%) to influencing river water's hydrochemistry. These outcomes give detailed information to understand the water quality affecting factors in the Ganga River system. The management and remedial practices are an urgent task required to conserve WQ in the upstream region to check WQ's further deterioration in the future.