The met department predicted more rains over the next two days in northern India.
Officials continued with the rescue operations in rain-hit areas as the toll in the two states climbed to 58. While 40 perished in the torrential downpour in Uttarakhand, 18 people died in Saharanpur district of UP.
Sources say more than 58,000 people are stranded at different places on the route of the Chardham Yatra - Yamunotri, Gangotri, Badrinath and Kedarnath.
The onward trip to Hemkunt Saheb - the sacred pilgrimage for Sikhs - has also been abandoned for now, officials say.
At many places while the gushing rivers have washed away roads and caused landslides, flood waters has entered several villages on banks of the Alaknanda river.
The Kailash Mansarovar Yatra has also been stopped for now.
The Ganga is flowing two metres above the danger mark and an alert has been sounded and people have been asked to desist from bathing in the holy river.
Army officials say bases have been made for rescue operations in Bareilly and Sarsawa.
Members of the National Disaster Response Force (NDRF) are however unable to move further from Dehradun owing to inclement weather.
Fourteen choppers of the Indian Army have also been put on standby for rescue operations.
Uttarakhand Chief Minister Vijay Bahuguna while admitting that the situation was "grave", told IANS that the government was working swiftly to rescue people stranded at different places and providing relief to the flood effected areas.
The public works department (PWD) of Uttarakhand has confirmed "serious damage" to 450 roads in the state.
Regional Met director of Uttarakhand Anand Sharma said the situation might slightly improve from Tuesday evening onwards as the rains are likely to subside.
Several trains, including Sriganganagar Express, Hemkund Express and Janshatabdi have been cancelled due to flooding of tracks, a railway official told IANS.
Incessant rains in Nainital since Monday has raised the level of the lake by five feet and most tourists were forced to spend their holiday indoors.
In Uttar Pradesh, the Malan and Ganga rivers are in spate in western parts of the state and the army has been called in Mandawar and Rawli areas of Bijnore.
Several houses collapsed in Sardhana area of Meerut while 18 people were killed in Saharanpur in roof collapse and a car was washed away by rain water.