Sandhaya Kureel, a spokeswoman of the Disaster Management and Relief Department, said most of the 59 fatalities were caused by house collapses, lightning and drowning in Uttar Pradesh state. They included at least five people dying of snake bites in flooded areas.
The temple city of Varanasi was lashed by 19 centimetres (7 inches) of rain on Thursday and Friday, flooding the bathing areas of the Ganges River used by thousands of Hindu pilgrims.
Schools were shut on Saturday as the downpour caused disruptions in the state capital, Lucknow, and several towns, including Amethi and Hardoi.
J.P. Gupta, director of the state Meteorological Department, said the rain is expected to ebb after Monday.
The Press Trust of India news agency said the western state of Maharashtra also was hit by heavy rain and nearly 3,000 people were moved to higher ground due to flooding in low-lying areas of Pune city and neighbouring areas.
More than 350 people have been killed by rain-related causes in India, Nepal and Bangladesh this monsoon season, which runs from June through September.