In Masters competition, Whanganui was third, just behind Mana.
The Under-18 class saw Whanganui finish second with 304.5 points, behind Poverty Bay's 437.5.
New Zealand Under-23 representatives Max Brown and Aiden Nositter will race open class today through to Sunday at the Australian GP2 event.
Toby Brooke and Erica Tanner will also compete at Under-18 level, in what will be Tanner's international debut.
"It's more about seeing where they are against world class competition and getting some international race experience at that level," said clubman Peter Brown.
At Lake Karapiro, the 17-year-old Brooke had the biggest medal haul with nine, including three gold of which two were in the Open Men's class.
The top performing female was Masters woman Robyn Scott, with seven medals, closely followed by Kylie Gibson with six.
Amongst the Under-14s, Lucas Thompson secured three medals in a great effort at his first nationals, while top Under-16 performer was Regan Davey with five medals.
"Back on the Whanganui river this weekend it's more about building again for this season and the future" said Brown.
"We have a whole load of youngsters beating the door down to try kayaking, so they get that chance on Saturday at 10.30am with our intro-programme.
"At this stage we aren't sure we have enough kayaks to put them all in."