Pugh held on to claim the gold medal and finished in a time of 1 hour 9 minutes 41 seconds to Theobold's 1:09:43 with Manawatu's Paris Cutler third in 1:10:42.
It was double delight in Taupo for Pugh as she was awarded a second gold medal as NZ Secondary Schools Champion in the 14-15 year age group, representing Bethlehem College.
Kim Cadzow, 15, also from the Greerton Swim Club finished 12th in the same event after narrowly missing a medal finishing fourth in the NZ Secondary School 1km event the previous day.
In the non-championship events, Greerton Swimmers placed in the top three were Louis Fitzjohn over 1km, Brooke Ross in the 500m, along with Arianna Roberts and Will Quin in the 100m.