New Swans boss Carlos Carvalhal got his tenure off to a winning start courtesy of a late comeback victory at Vicarage Road, but he could now be without Naughton for the next three matches.
The defender appeared to stamp on the leg of Watford attacker Stefano Okaka during a scramble for the ball, although the incident was not seen by match officials at the time.
The FA has now decided to charge Naughton with violent conduct after reviewing video evidence, though, which could see the 29-year-old handed a three-game ban if found guilty.
Should that be the case then Naughton would miss Premier League matches against Tottenham Hotspur and Newcastle United either side of an FA Cup showdown with Wolverhampton Wanderers.
Naughton is one of only two outfield players to have started every Premier League game for Swansea so far this season.