The main stream of the Ganges begins at the confluence of the Bhagirathi and Alaknanda rivers in the town of Devprayag in the Garhwal division of the Indian state of Uttarakhand. The Bhagirathi is considered to be the source in Hindu culture and mythology, although the Alaknanda is longer, and, therefore, hydrologically the source stream. The headwaters of the Alakananda are formed by snowmelt from peaks such as Nanda Devi, Trisul, and Kamet. The Bhagirathi rises at the foot of Gangotri Glacier, at Gomukh, at an elevation of 3,892 m (12,769 ft), being mythologically referred to as, residing in the matted locks of Shiva, symbolically Tapovan, being a meadow of ethereal beauty at the feet of Mount Shivling, just 5 km (3.1 mi) away.

Although many small streams comprise the headwaters of the Ganges, the six longest and their five confluences are considered sacred. The six headstreams are the Alaknanda, Dhauliganga, Nandakini, Pindar, Mandakini, and Bhagirathi rivers. The five confluences, known as the Panch Prayag, are all along the Alaknanda. They are, in downstream order, Vishnuprayag, where the Dhauliganga joins the Alaknanda; Nandprayag, where the Nandakini joins; Karnaprayag, where the Pindar joins, Rudraprayag, where the Mandakini joins; and finally, Devprayag, where the Bhagirathi joins the Alaknanda to form the Ganges River proper.

After flowing 250 km (155.343 mi) through its narrow Himalayan valley, the Ganges emerges from the mountains at Rishikesh, then debouches onto the Gangetic Plain at the pilgrimage town of Haridwar. At Haridwar, a dam diverts some of its waters into the Ganges Canal, which irrigates the Doab region of Uttar Pradesh, whereas the river, whose course has been roughly southwest until this point, now begins to flow southeast through the plains of northern India.

The Ganges follows an 800 km (500 mi) arching course passing through the cities of Kannauj, Farukhabad, and Kanpur. Along the way it is joined by the Ramganga, which contributes an average annual flow of about 500 m³/s (18,000 cu ft/s). The Ganges joins the Yamuna at the Triveni Sangam at Allahabad, a holy confluence in Hinduism. At their confluence the Yamuna is larger than the Ganges, contributing about 2,950 m³/s (104,000 cu ft/s), or about 58.5% of the combined flow.

Now flowing east, the river meets the Tamsa River (also called Tons), which flows north from the Kaimur Range and contributes an average flow of about 190 m³/s (6,700 cu ft/s). After the Tamsa the Gomti River joins, flowing south from the Himalayas. The Gomti contributes an average annual flow of about 234 m³/s (8,300 cu ft/s). Then the Ghaghara River (Karnali River), also flowing south from the Himalayas of Nepal, joins. The Ghaghara (Karnali), with its average annual flow of about 2,990 m³/s (106,000 cu ft/s), is the largest tributary of the Ganges. After the Ghaghara (Karnali) confluence the Ganges is joined from the south by the Son River, contributing about 1,000 m³/s (35,000 cu ft/s). The Gandaki River, then the Kosi River, join from the north flowing from Nepal, contributing about 1,654 m³/s (58,400 cu ft/s) and 2,166 m³/s (76,500 cu ft/s), respectively. The Kosi is the third largest tributary of the Ganges, after the Ghaghara (Karnali) and Yamuna.The Kosi merges into the Ganges near Kursela in Bihar.

Along the way between Allahabad and Malda, West Bengal, the Ganges passes the towns of Chunar, Mirzapur, Varanasi, Ghazipur, Patna, Hajipur, Chapra, Bhagalpur, Ballia, Buxar, Simaria, Sultanganj, and Saidpur. At Bhagalpur, the river begins to flow south-southeast and at Pakur, it begins its attrition with the branching away of its first distributary, the Bh?girathi-Hooghly, which goes on to become the Hooghly River. Just before the border with Bangladesh the Farakka Barrage controls the flow of the Ganges, diverting some of the water into a feeder canal linked to the Hooghly for the purpose of keeping it relatively silt-free. The Hooghly River is formed by the confluence of the Bhagirathi River and Jalangi River at Nabadwip, and Hooghly has a number of tributaries of its own. The largest is the Damodar River, which is 541 km (336 mi) long, with a drainage basin of 25,820 km² (9,970 sq mi). The Hooghly River empties into the Bay of Bengal near Sagar Island. Between Malda and the Bay of Bengal, the Hooghly river passes the towns and cities of Murshidabad, Nabadwip, Kolkata and Howrah.

After entering Bangladesh, the main branch of the Ganges is known as the Padma. The Padma is joined by the Jamuna River, the largest distributary of the Brahmaputra. Further downstream, the Padma joins the Meghna River, the second largest distributary of the Brahmaputra, and