Mana clocked 1:05:41 in qualifying round to better her earlier national record of 1:05:47 before bagging the gold in the finals.
Meanwhile, Sajan Prakash won the gold medal in men's 400m freestyle competition.
Over 700 swimmers from across the country are taking part in championship organised jointly by the Swimming Federation of India (SFI) and Gujrat State Aquatic Association (GSAA).
The five-day long championship was inaugurated by former Goa Chief Minister Digambar Kamat, who is also the president of SFI.