Nataraj won four golds, one silver and created three New Meet records, while Kataria won four golds and two new records.
Nataraj, who won the Individual Championships at the Junior Nationals earlier in Pune, also qualified for the Youth Olympics to be held in Buenos Aires in November next year. He edged Sajjan Prakash, who won 5 golds and had 2 meet records.
Kataria (4:28.29) of Haryana beat Karnataka's Malavika V to win gold in the 400m Freestyle, while 15-year-old Khushi Dinesh of Karnataka won bronze with a time of 4:36.59.
The Men's Championships was won by Railways with 139 points, while Karnataka emerged victories in the women's event with a score of 133 points.
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The Diving Championship was won by Services and Railways with 34 and 31 points respectively in men's and women's section.
Earlier in water polo, Maharashtra and Railways won the gold in the women's and men's section respectively while Police and Services won the silver.
Current National record holder Saurabh Sangvekar from Railways won the 800m Freestyle race leading the event for the most part with a time of 8:23.84.
Sajan Prakash of Kerala lead from start to finish in his favourite 200m Butterfly to win his 5th gold of the event with a new record time of 1:59.12. Supriyo Mondal (2:02.91) of RSPB won silver and Karnataka's Avinash Mani (2:03.27) bagged the bronze medal.
Delhi's Richa Mishra (2:22.86) won her third gold in the 200m Butterfly for women. She finished ahead of Damini Gowda (2:24.08) of Karnataka who won silver, while Trisha Kharkhanis (2:27.06) of Maharashtra won bronze.
Meenakshi V K R (1:07.27) of Tamil Nadu defended a late surge from Yuga Birnale (1:07.68) of Maharashtra to win the 100m Backstroke. Youngster Suvana C Bhaskar (1:08.31) won the bronze medal.