"May the festival bring joy and prosperity to all sections of our people across the length and breadth of the country," Mukherjee tweeted.
He added, "I urge all Indians to celebrate Diwali in a pollution free manner."
Prime Minister Narendra Modi and Congress Vice President Rahul Gandhi also wished the country on eve.
Modi wished people in India and across the world a happy Diwali.
In a video message, Rahul wished the country a prosperous and happy Diwali.