The Tickford driver was a late improver in the half-hour session, jumping to the top inside the last two minutes with a 53.989s.
That was the only time under the 54s bracket and gave Waters a comfortable 0.17s margin over second-fastest Anton De Pasquale.
"The track is degrading which you would expect," said Waters of the two-year break from racing in WA. "It's more just how much it's going to degrade.
"Our team did a good job having a good plan for practice and we executed that. We've got a fast car, hopefully we can keep moving forward."
Jack Le Brocq was third fastest for Matt Stone Racing while David Reynolds continued his good form with the fourth quickest time.
Brodie Kostecki was fifth fastest ahead of Will Davison while Macauley Jones led the way for Brad Jones Racing in seventh.
Chris Pither was an impressive eighth fastest for PremiAir Racing as Tim Slade, who was fastest with three minutes to go, slipped back to ninth at the flag.
There were plenty of big names off the pace, led by series leader Shane van Gisbergen. The Kiwi was fastest for most of the session, but dropped back to 13th in the closing minutes after not improving on his final run.
James Courtney had an action-packed session that included a wild off at the left-hander and a trip through the sand at Turn 7 after being hit from behind by Todd Hazelwood. He ended up 14th fastest.
Title contender Chaz Mostert was just 19th fastest while Triple Eight driver Broc Feeney was 25th and last after not running new rubber.
