They arrived at Jollygrant airport here in the evening and were received by Chief Minister Vijay Bahuguna and British High Commissioner to India James David Bevan.
The royal couple joined in the Ganga aarti held at Parmartha Niketan Ashram for the peace of those who died in the June flash floods in the state.
"It is my first visit to the Ganges, so from that point of view it is a very special occasion for both myself and my wife," Charles said later, according to a Clarence House tweet.
This is the third official visit to India by the couple, and their most extensive.
Dehradun will be the most important leg of their India tour as they visit three world renowned institutions in the city: The Indian Military Academy, The Forest Research Institute and the Doon School, where local women are being helped to finance their own self-employment projects.
The royal couple's India visit ends Nov 14 when they leave for Sri Lanka for the Commonwealth Heads of Government Meeting (CHOGM) in Colombo.