Manaaki, 17, said it was quite sad to have raced his last secondary school nationals but he was proud of his team.
He said winning the last race of the day and event today, the under-19 boys' W6 250m final, was a great feeling.
"I looked over my shoulder after about 220m and we had a good, three-seat lead on them, and that was when I knew we had done enough to get home and win gold," he said."It felt great, it is not something you can describe."
Manaaki also won a gold medal as a solo paddler on Tuesday but said he felt prouder about the team title. "I prefer the team gold because everyone on the boat is so happy, and you are all exhausted for each other."
Rotorua Boys' High School's younger team, the W6 under-16 crew, also won gold today in their 250m final, proving there is plenty of talent coming through at the school.
"All the teams [at our school] train together and push each other along," Manaaki said. "It is great to see the new, younger ones coming through and doing well."
While the Boys' High under-19 team have raced their last major race for the school, the boys will represent local club Hei Matau Paddlers at the world champs in Australia next month.
Manaaki said they had been training since the end of last season, virtually without a break, to prepare for the world champs.
Other Rotorua schools also picked up medals at the Te Wananga o Aotearoa National Secondary School Waka Ama Championships including Rotorua Girls' High School, Ruamata, and Rotorua Lakes High School.
The four-day competition is one of the largest secondary school sports events in New Zealand - second only to rowing's Maadi Cup, which was also held this week.
List of medals won by Rotorua schools:
Rotorua Girls' High School: Bronze medal (U16 Girls' W6 250m), bronze medal (U16 Girls' W6 500m).
Rotorua Lakes High School: Silver medal (Kyra Mita, U16 Girls' W1 250m).
Ruamata: Silver medal (U16 Boys' W6 500m).
Rotorua Boys' High School: Gold medal (U19 Boys' W6 250m), gold medal (U19 Boys' W6 500m), gold medal (U16 Boys' W6 250m), gold medal (Manaaki Te Kowhai, U19 Boys' W1 250m).
Composite: Bronze medal (Rotorua Boys' High School and Rotorua Girls' High School, U16 Mixed W12 250m).