Traffic and track position were issues across both qualifying sessions on the short Symmons Plains layout, with a two critical to fight for pole.
In both sessions Waters was in the fight for pole, and set purple sectors on his final, only to trip over DJR cars at turn 6.
In the first session he had gone purple in the first sector before getting a tow off Anton De Pasquale down the back straight and then making contact with the #11 Mustang.
That meant Waters didn't improve and he ended up 1oth on the grid.
The same thing then happened in the second session, Waters going purple in sectors 1 and 2 before running into Will Davison at turn 6.
Waters did manage to qualify third, but the contact cost him a clear shot at pole.
Speaking after the session Waters was unapologetic for his forceful driving.
"It's just hard because everyone is trying to get a tow and there's people playing games," Waters told Fox Sports.
"It creates so much congestion out there. It's always going to happen, you're going to have things like that.
"I was on good laps and caught a DJR car both times. I don't know if they were making mistakes or just generally that slow. If they are that slow, I feel really bad for the drivers.
"I was on a good lap and had no choice but to get it done. It is what it is. It probably cost myself a few spots, cost those guys a few spots.
"If I'd got that last lap, I probably would have been on pole, which would have been nice. But it is what it is."
Waters' efforts didn't sit well with DJR team principal Ben Croke, though.
"It's not the smartest thing that he's probably ever done," Croke told the broadcast. "If him out on track, or his team, can't manage the gaps to the car in front in qualifying, to just to run into the car in front because he's frustrated is probably not really appropriate."
Davison, meanwhile, had a measured response to his run-in with Waters, despite conceding that it cost him positions.
"I was on my best lap for sure, so we would have jumped up a long way further than we were," he said.
"Cam obviously got a monster tow up the back straight and he does that, he follows very close to maximise his tow down the back straight. But I can't disappear.
"He tried to pass me and I felt a bit whack. Annoying, but I get it from both sides. I'm sure he's annoyed too.
"But that's the nature of 25 cars out there and there's not enough room, so you've got to pick your gaps. You want a tow but you know if you get too close, the car is in your way in the braking zone. It's always a compromise."
