The dramatic incident will take place in episode ten of the current series, which airs next week before the BBC One show goes on a break.
Connor snaps when his alcoholic mother Christine discovers that he is planning to run away with his girlfriend Imogen (Kirstie Steele).
O'Meara told Inside Soap: "Things have finally hit a peak between Christine and Connor. Connor and his girlfriend Imogen are planning to run away, but Christine gets wind of it. When she tries to stop them, Connor just snaps. It's going to be a shock for the viewers.
"In his frustration, Connor starts another fire - but this one is going to have very serious consequences for all three of them. Things won't be the same again."
Former EastEnders star Laurie Brett, who plays Christine, added that the repercussions of the blaze will run into next year.
Brett said: "Next series will be a big one. There'll be huge fallout from the fire, and a lot more drama to come for Connor and Christine."
Waterloo Road airs on Thursdays at 8pm on BBC One.