Waddell improved on her fourth placing last year to dominate the women's contest over 25kms in 34:53.59. It also ensured the time trial title remained in Cambridge, following on from Melissa Holt who won for the past three years but bypassed the championships this year.
Waddell finished 20 seconds ahead of fellow Waikato rider Jaime Nielsen and Commonwealth Games gold medallist Alison Shanks by 33 seconds.
"I was really thrilled with that one today. I've been getting some seconds and thirds in recent times so it was great to crack the win especially at this level," Waddell said.
"This is huge for me. This is the biggest event in New Zealand and a very quality field. The BikeNZ system is in such good stead that it is producing some very good athletes so to be able to line up and go faster than them is a pretty cool achievement."
Waddell said she will also compete in the road race championships before returning to the para cycling programme on the tandem at the world track and road championships with blind cyclist Jane Parsons. She also mixes cycling with a busy life as mother of three children on the family farm in Cambridge.
Saturday’s women's road race over eight laps and 123kms of the demanding circuit in Cashmere Hills-Hoon Hay where S series champion Cath Cheatley (Wanganui) is chasing her third title in a strong field including Jo Kiesanowski (Christchurch), defending champion Rushlee Buchanan and fellow Commonwealth Games rider Kaytee Boyd (Auckland), national series champion Serena Sheridan and mountain star Rosara Joseph.
Get The Leadout Newsletter
The latest race content, interviews, features, reviews and expert buying guides, direct to your inbox!
With 1,500 watts of peak power, the Amflow PX Carbon Pro is the most powerful electric mountain bike you can ride on the trails, but is it too much oomph?
