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Heaton, a pupil at John McGlashan College, won the gold medal at the New Zealand short-course spring championships in 16min 27.40sec.
It beat the record Kane Radford (Rotorua) set in 2004 by 8sec, and was a personal best time by 16sec.
"Thomas is a very mature swimmer which is unusual for a person of his age," coach Andy Adair told the Otago Daily Times from Wellington.
This was demonstrated by his 500m split times of 5min 32sec, 5min 28sec and 5min 26 sec.
"We like to get our swimmers to do negative splits," Adair said. "Thomas did this today and came home strongly in the last few laps."
Heaton won his second gold medal in the 400m freestyle in a personal-best 4min 19.46sec.
He also collected silver medals in the 200m freestyle (2min 05.49sec) and 400m individual medley (4min 58.56sec).
It has been a good championships for the Waves club.
Carina Doyle won three bronze medals in the women's aged 17 and 18 freestyle events - 100m (57.45sec), 800m (8min 51.32sec) and 400m - and Chris Dickie won a bronze medal in the men's aged-16 50m breaststroke.
Sophie Gibson became the first Queenstown female swimmer to win medals at the short-course spring championships when she won a silver medal in the girls aged 14 200m backstroke (2min 22.80sec) and a bronze medal in the 200m butterfly (2min 25.91sec). They were both personal bests.
Kurt Crosland (Neptune) broke double Olympian Danyon Loader's 1998 Otago senior men's record when he won the men's open 200m individual medley in 2min 00.82sec in the heat and 1min 58.68sec in the final. Loader's time was 2min 00.89sec.
Crosland also broke an Otago record in the 50m butterfly when he won the bronze medal in 24.55sec.
Katie Kenneally (Neptune) broke Olympian Anna Wilson's 1995 Otago 100m individual medley women's open record with her time of 1min 03.65sec when she won the silver medal.
Kate Godfrey (Neptune) won silver medals in the women's aged 17 and 18 and open 200m backstroke, setting an Otago open record of 2min 10.16sec.
Andrew Trembath (Neptune) won gold medals in the boys aged 15 grade in the 50m butterfly (25.96sec) and 200m individual medley (2min 06.16sec in heat and 2min 05.97sec in final) and a silver medal in the 200m breaststroke (2min 22.53sec).
They were all Otago records.
It was another good day for Gennadiy Labara's Osca squad and the Neptune club which won five gold, four silver and two bronze medals and broke nine Otago records.
Han Zhang (Neptune) won a gold medal in the boys aged 14 200m breaststroke (2min 24.66sec) and a silver medal in the 200m individual medley.
Jeremy Hopkins (Neptune) won a gold medal in that event.