The ship and her 225 crew members left at 10 a.m.
HMCS Toronto is being deployed to the Arabian Sea as part of Operation Artemis, Canada's contribution to security and counter-terrorism operations in the region.
Canada is one of 26 countries contributing naval assets to the international waters of the Middle East, which has some of the world's most important shipping lanes.
Mary Berrigan was at the dockyard on Monday to see off her son, Leading Seaman Andrew Berrigan.
"I'm just a little nervous," she told CBC News.
"I'm hoping he's going to be safe and come back to us."
The Royal Canadian Navy said Operation Artemis could see HMCS Toronto deployed for more than 200 days.
Emily Hatcher, who works with the Halifax and Region Military Family Resource Centre, said resources are available to all family members prior to, during and after deployments.
"Whenever a ship leaves, we set up a family network of military family members experiencing the deployment who come together on a monthly basis and plan activities for all members, all family members experiencing the deployment," she told CBC News.
"What we strive to do during any deployment is keep families informed, supported and connected and really offer them opportunities to get together and know one another with the people who share that same experience."