Gilbert left the field in the hands of trainers in the third quarter of Friday night's loss to Collingwood after planting his left knee and twisting awkwardly.
He was subbed out of the game shortly after, and the club is optimistic he hasn't suffered a major ligament strain.
"We don't think so at this stage," Watters said post-game.
"But I think we've had some examples even in recent weeks where people are saying it's not an ACL and all of a sudden it is. You've just got to wait for the scan. Anything else is just speculation really."
The Saints are also unsure if veteran Lenny Hayes will miss any further games with the tight calf muscle that kept him out of the Magpies clash.
Hayes was injured in the warm-up and was replaced by Jack Newnes, who collected 12 disposals.
Watters said Hayes perhaps could have still played, but the Saints wanted to err on the side of caution with the 33-year-old.
"Calf tightness [or] minor strain? We'll know when it's fully assessed with a scan tomorrow," Watters said.
"It just pulled up in the warm-up, and it was touch-and-go, but if you run the risk at that point … it can turn into four or five [weeks] pretty quickly."
Although the Saints fell to their fifth loss of the year with the 26-point defeat, Watters was encouraged by elements of the performance.
The Saints had only two fewer contested possessions than the Magpies, one fewer clearance, and three fewer inside-50 entries, with Watters identifying a four-quarter effort as the major area for improvement.
"To beat good sides it's more than three quarters, you've got to go the full distance," he said.
"You have to capitalise when you have your set shots, when you have your opportunities. There's some good stuff to take out of it, but we want to be a club that strives to beat the good sides, and you need to go the full distance. It's a good learning experience for a lot of our players."
Captain Nick Riewoldt was again the Saints' best player in the defeat, kicking four goals and taking 11 marks.
Watters lauded the skipper's leadership as the club moves into a new phase with a number of inexperienced players in the side.
"They get to see first-hand what it means to be a pro," Watters said.
"There's a lot of great players, but there's very few players who just through sheer will try to pull their side across the line. I take my hat off to the way he's playing and the way he's leading."
Follow AFL website reporter Callum Twomey on Twitter at @AFL_CalTwomey.
