The water reaches Rajasthan through Harike Barrage and distributed further by the Indira Gandhi Feeder (IGF) and other canals.
In a letter to Badal, she said the water, hazardous to health, is being used for drinking purposes by a large population in eight districts in western Rajasthan and causing water-borne diseases.
Raje also sought legal action against the industrial units and local bodies responsible for severely polluting the Sutlej waters, according to a release here.
As per the letter, Rajasthan took up the matter on several occasions with the government of Punjab, but the problem was not resolved.
Raje said the Chief Secretary of Rajasthan had also written to his Punjab counterpart in January and November last year requesting the PSPCB to act upon the Central Pollution Control Board's report of 2012, which had highlighted gravity of the issue.