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The Otago team won 16 medals - one gold, eight silver and seven bronze - for its best team performance since 1996.
That was when Duncan Laing was the coach and Olympians Danyon Loader, Anna Wilson and Scott Cameron were in the team.
Last year Otago swimmers won six medals - three silver and three bronze.
In 2011, Otago swimmers won just three medals - two silver and one bronze.
The medallists in Auckland last week were all members of coach Gennadiy Labara's Osca squad.
Godfrey (19), who has been part of the Osca squad for the past six years, won Otago's only gold medal at the championships in the 200m individual medley in 2min 17.87sec.
It was one of her three qualifying times for the World University Games at Kazan, Russia, in July. The others were in the 100m backstroke (1min 03.04sec) and the 200m backstroke (2min 15.46sec) when she won silver medals.
On the last night of finals, Godfrey won the silver medal in the 200m backstroke and a bronze medal in the 400m individual medley in 4min 54.97sec.
The other medal on the final night was won by the Neptune team of Nick Tyrrell, Adam Simpson, Rhys Applegarth and Kurt Crosland which won a bronze medal in the 4 x100m freestyle relay.
Godfrey won five medals - one gold, three silver and one bronze. She broke four Otago senior women's records.
Crosland won four individual medals - two silver and two bronze - and broke nine Otago senior men's records.
The other individual medallist was Matthew Glassford (Neptune) who won a bronze medal in the 200m breaststroke in 2min 17.01sec. It was one of his two Otago records.
Crosland and Glassford were key members of Otago and Neptune relay teams that won six medals - three silver and three bronze.
The other members of the relay teams were Tyrrell, Applegarth, Jeremy Tasker and Simpson.
The Neptune club was third on the points table of the 44 clubs which registered points at the championships.