Bharti, who has been involved for the last few months in a campaign to protect the Ganga, apprised Mukherjee of the need for ensuring uninterrupted flow of Ganga downstream from Tehri dam.
In a memorandum, the BJP leaders said two solutions had been suggested earlier.
The first is construction of a 45 km tunnel from Dharasu to Koteshwar that would ensure smooth flow of the Ganga.
The other alternative is to create a small channel through the dam itself which would ensure smooth flow.
The two leaders suggested that a committee can be formed to look into the whole issue and suggest some other solutions if need be.
Bharti and Advani also raised the need to protect the "sanctity and security" of the ancient Dhari Devi temple situated on the Alaknanda river near Srinagar in Uttarakhand.
"The existence of Dhari Devi temple is in danger due to the construction of a dam on Srinagar hydro-power project on Alaknanda," they said in another memorandum.
The BJP leaders maintained that earlier the project was for 200 MW which did not pose any danger to the temple.
They said the project capacity was later increased under "dubious circumstances" bringing the temple under threat of submergence.
The BJP leaders sought Mukherjee's intervention in the matter.