But Waterfield stole the limelight, opening with three perfect 10s.
Daley was guilty of over-rotating on his armstand triple somersault dive and was unable to overturn the 40-point deficit going into the last dive.
"I'm sure the world champion is meant to win the British Championships but that is why diving is an on-the-day sport.
"I did make silly mistakes but then that's what happens in diving and hopefully I can correct them. I'm sure I am never going to make them again because I don't like feeling like this."
The 'twister' was invented by Leon Taylor, a former Olympic silver medallist and Daley's friend and mentor, in 1998 and takes 1.8 seconds from leaving the platform to hitting the water at 30mph.
After failing to win a national competition for the first time since 2006, Daley said: "I'm going to be disappointed with second but it has to happen some time and I'm glad it's at a nationals rather than an international competition.
He described Waterfield as "an incredible diver", adding: "I'm going to go home and work my socks off. It's given me the kick up the backside I needed."
It was a triumphant return for Waterfield, winner of Olympic silver with Taylor in the 10m synchro four years ago, competing in the platform competition for the first time since the Beijing Games.
Max Brick (right) was third behind Waterfield (centre) and Daley
After adding to his world medals and a Commonwealth title, the 28-year-old Southampton diver said: "I've got a big year with the Commonwealths and the World Cup so to put in a good performance gives me a big confidence boost for the rest of the year."
Daley will now set his sights on adding the Commonwealth crown to his growing list of titles when Delhi hosts the Games in October after being deemed too young at the 2006 Games.
Daley's coach Andy Banks remained upbeat with his diver's display, saying: "Tom's new dive went better than it has done in training.
"I'm not that disappointed because there is a lot of good that can be taken out of what we are doing and I also know what the next part of the plan is."
Rebecca Gallantree claimed her third title of the meet when she beat Jessica Williams to win the 3m springboard with 305.80 points. The 13-year-old Grace Reid was third.
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