According to the reports of CPCB and SPCB, what are the main sources of pollution in rivers in India?

Organic and bacterial contamination.

The Central Pollution Control Board (CPCB) in collaboration with State Pollution Control Boards has been monitoring water quality of national aquatic resources at 507 stations. The data obtained from these stations show that organic and bacterial contamination continues to be the main source of pollution in rivers. The Yamuna river is the most polluted river in the country between Delhi and Etawah. Other severely polluted rivers are: the Sabarmati at Ahmedabad, the Gomti at Lucknow, the Kali, the Adyar, the Cooum (entire stretches), the Vaigai at Madurai and the Musi of Hyderabad and the Ganga at Kanpur and Varanasi.