The FA said it amounts to improper conduct and Emery has until 18:00 GMT on 2 January to respond to the charge.
The Spaniard apologised for the incident, which was not included in the officials’ match report.
“I said to them I’m sorry,” Emery said after the game.
“It wasn’t hard but it touched one supporter.”
Emery went to speak to the home supporter immediately after the incident and again at full-time.
Speaking in his news conference on Thursday, Emery said he hoped the apology would be the end of the matter.
“I kicked the bottle in frustration but not at the supporters, not with this intention. It’s circumstances. I apologised. I hope it’s the end of the matter, yes,” he said.
Pierre-Emerick Aubameyang had given the Gunners a seventh-minute lead in the Premier League match at the Amex Stadium and the visitors dominated much of the first half.
But a mistake by right-back Stephan Lichtsteiner allowed Jurgen Locadia to equalise for Brighton in the 35th minute.
Emery was disappointed by his team’s second-half display and took his frustration out on the water bottle on the touchline.
After apologising to the Seagulls fan, Emery appeared to explain his actions to the fourth official.
The officials had not included the incident in the match report as they were happy with the way it had been handled.
Former Manchester United manager Jose Mourinho was given a one-match ban after being sent off for kicking a water bottle down the touchline during his side’s Premier League game against West Ham in 2016.