Waters' 2013 campaign was brought to a swift end last July when he underwent shoulder surgery.
The 27-year-old was dealt a further blow before Christmas when his shoulder became infected, forcing surgeons to prematurely remove the pins they had inserted.
It remains unclear whether the pins were inserted long enough for Waters' shoulder to heal, with the Eagles to take a wait-and-see approach over the next fortnight.
"The procedure he had was successful. But there was a little bit of an infection in the shoulder," coach Adam Simpson said of Waters, who has played just 120 games over 13 seasons.
"They had to take the screws out.
"Hopefully it's been in long enough.
"He's a 50-50 chance for whether he needs another bout of surgery or not. It could be a lengthy one if he needs it."
Waters' latest setback is almost certain to end any chance he had of taking on the captaincy this year.
Simpson said the leadership group and captaincy would be decided by the end of January, with Darren Glass expected to be appointed skipper for the seventh straight year.
Ruckman Nic Naitanui ran laps at pre-season training on Monday as he builds up his fitness and strength following a year of groin issues.
Simpson said he would assess Naitanui's availability for the NAB Challenge closer to the time.
"He's progressing well," Simpson said of the 2012 All-Australian.
"We actually trained on Saturday and I had a good look over and he's running as best I have seen.
"So we hope to progress him to full training by the end of January."
Troubled midfielder Murray Newman is training with the main group despite his future being up in the air after he was found guilty of assault.
The 20-year-old, who was delisted by the Eagles in November before being drafted onto their rookie list, will be sentenced in March.
"We stick by him and we knew potentially this might happen, so nothing changes there from the club's point of view," Simpson said.