After originating from the Gangotri Glacier at Goumukh in Garhwal Himalayas in Uttarakhand as the River Bhagirathi, the main stream of the River Ganga begins at the confluence of the Bhagirathi and Alaknanda rivers in the town of Devaprayag of the Indian State of Uttarakhand. The headwaters of the River Alaknanda are formed by snowmelt from peaks such as Nanda Devi, Trishul and Kamet.

Although many small streams contribute to the headwaters of the Ganga, six longest and their five confluences are considered sacred and important. The six headstreams are: Alaknanda, Dhauliganga, Nandakini, Pindar, Mandakini and Bhagirathi. The five confluences, known as the Panch Prayag, are all along the Alaknanda. From up to downstream order, they are: 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 Ganga.

After flowing 250 km through mountains, Ganga finally emerges in the plains at Rishikesh. At Haridwar, it is dammed at Bheemgoda Dam, from where some of its water gets diverted into the Ganga Canal, whereas the river, whose course has been roughly southwest until this point, now begins to flow southeast through the plains of northern India. The Ganga River follows an 800 km course passing through the cities of Kannauj, Farrukhabad and Kanpur. Along the way it is joined by the River Ramganga near Kannauj. Ganga is joined by the River Yamuna at Prayagraj. At their confluence at Prayagraj, the Yamuna is larger than the Ganga, contributing about 58.5 percent of the combined flow. Now flowing east, Ganga river meets the Tons River (ancient name Tamsa) at Sirsa, about 311 km downstream of Prayagraj. After the Tons, the Gomti River joins Ganga near Saidpur, Kaithi in Varanasi district. Then the Ghaghra River, also flowing south from the Himalayas of Nepal, joins. The largest tributary of the Ganges, it is known as Karnali in Nepal.

Next important river to join is the Son River. It is the principal southern tributary of the Ganga River, which rises in the state of Madhya Pradesh. It flows north past Manpur and then turns northeast. The river joins the Ganga above Patna. The Gandaki River and the Kosi River from Nepal also join Ganga with massive inflow. In fact, Kosi is the third largest tributary of the Ganga, after Ghaghara and Yamuna. Kosi River merges into Ganga near Kursela in Bihar. Along the way between Prayagraj in Uttar Pradesh and Malda in West Bengal, the Ganga River passes through the towns of Chunar, Mirzapur, Varanasi, Ghazipur, Ballin, Buxar, Chapra, Hajipur, Patna, Bhagalpur and many others. 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 Bhagirathi-Hooghly which goes on to become the Hooghly River.

Just before the border with Bangladesh, the Farakka Barrage controls the flow of Ganga, 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. River Hooghly also has a number of tributaries of its own. The largest is the Damodar River. Between Malda and the Bay of Bengal, Hooghly River passes the towns and cities of Murshidabad, Nabadwip, Kolkata and Howrah. Finally; the Hooghly River empties into the Bay of Bengal near the Sagar Island.