After being restricted to 80 rotations a match through the pre-season competition, teams reverted to high interchange numbers in round one, with the Saints recording 121 in their 13-point loss to Gold Coast.
Watters said the pre-season interchange rules placed pressure on players when they made the transition from playing "an endurance game" in the NAB Cup to being used in high-intensity bursts in the season proper.
"There was an enormous amount of cramping last week from all sides and across the whole AFL," he said on Tuesday.
"I think there were 12 players at Gold Coast that cramped and we had 13 or 14.
"Eighty rotations is very different to 130-140. Players need to operate at different levels of capacity.
"With 120-140 rotations, players are probably going for six to eight minutes at a higher intensity.
"That's very different to playing at 80 rotations; it becomes more of an endurance game. It's a different type of running."
St Kilda rotated players heavily in its final practice match against Greater Western Sydney, using the interchange 183 times with unlimited players on the bench.
Watters said it was "the anomaly of the pre-season competition at the moment" that teams prepared for round one under different rules than they would face in the season proper.
"Dealing with that difference poses challenges to every single side that's out there," he said.
"It's not a whinge, that's the reality, but it has an impact.
"My personal preference is to train and play how you're going to train and play come round one."
St Kilda is preparing for Friday night's clash against Richmond at the MCG with a six-day break and Watters said recovery would be paramount this week.
The Saints held their main session for the week at Linen House Centre on Tuesday morning, with defenders Sean Dempster (hamstring) and Sam Fisher (foot) both pushing to prove their fitness.
Watters expected Dempster to be available, while Fisher would need to be assessed, with Justin Koschitzke and Adam Schneider also in contention to come into the team after showing form with Sandringham.
"He (Koschitzke) played pretty well last week and made some really good forward 50 tackles, some good pressure, got involved and his leadership was really strong," Watters said.
"He's done everything to certainly push his name forward and he'll be amongst 24-25 that we select from. He's done the right things by his performance.
"[Schneider] is now building towards the type of game time that we need from him to be able to be considered … he's getting close."
Adam Schneider is a forward in NAB AFL Fantasy. He averaged 67.5 points in 2012. Register your team at our AFL Fantasy Hub .
Nathan Schmook is a reporter for AFL Media. Follow him on Twitter: @AFL_Nathan
