The Tickford driver emerged on top of what was effectively a quartet of qualifying sessions under the confusing Group A/B system.
He set a 50.764s in his eight-minute heat for the Race 2 grid, which put him on top of Group A.
Nobody in Group B was able to run it down either, Jamie Whincup going closest with a 50.866s.
For the Race 3 grid it was an all-Group A battle at the front, Waters going up against former teammate and fierce rival Chaz Mostert.
The pair were separated by just 0.01s at the end of the five-minute session as Waters took a second-straight pole with a 50.562s.
Speaking post-session Waters said he was surprised by the pole sweep, and that there’s still question marks over his tyre life for the races.
“The car has improved a little but over night,” he said. “In the first session I didn’t get everything out of it, then I did a much better job in the second one. I’m a little bit surprised to get both poles.
“A bit of tyre life would be awesome. We’re really good over one lap, we have been all year. But as soon as we get in the races, the other cars look after their tyres better than what ours can.
“We’ve done a few things overnight, hopefully we’ve gone in the right direction.”
Group B runner Anton De Pasquale was third in both sessions, while fourth threw up a surprise for each race. Erebus rookie Will Brown will start from the outside of the second row for Race 2, while Zane Goddard will do likewise in Race 3.
Whincup added to his second for Race 2 with a sixth for Race 3, however his teammate Shane van Gisbergen was uncharacteristically quiet. The Kiwi will have to come from sixth on the grid if he’s going to take an eighth-straight Supercars win in today’s first race, while he’ll start out of P7 for the second race.
The first of today’s two races starts at 1:35pm local time.
Qualifying – Race 2
Qualifying – Race 3