The former Liverpool player was dismissed on 81 minutes at The Valley after picking up a second yellow card for going in to a challenge with Addicks midfielder Diego Poyet with a high foot.
Riera reacted angrily to referee Darren Bond's decision and had to be dragged away by team-mates after confronting the official.
The 31-year-old has until 6pm on Tuesday, May 6 to respond to the FA charge.
Charlton won the match 3-1 to secure their Championship status, while Watford are comfortably in mid-table.
Riera joined Watford on a short-term deal at the end of March after being released by Turkish side Galatasaray in January.
The Spain international has an agreement to join Udinese - the other side controlled by Watford's owners - in the summer.