Embley, whose pre-season was interrupted by a hamstring injury, suffered the foot setback in the Eagles' 94-point win over Melbourne at the MCG on Saturday.
He will miss Saturday night's match against Carlton at Patersons Stadium as well as clashes against Port Adelaide (AAMI Stadium) and possibly the Western Bulldogs (Patersons Stadium).
Waters was a late withdrawal against the Demons after injuring himself in the warm-up and has been listed as a one- to two-week proposition on the club's official injury list.
In better news for the club, star ruckman Nic Naitanui, who is returning from groin surgery, trained lightly at Monday afternoon's session as he eyes a return in two to three weeks.
Defender Eric Mackenzie (hamstring) and midfielder Matt Rosa (thigh) face fitness tests ahead of Saturday night's clash with the Blues.