The couple in the vehicle became the focus of a police investigation after officers received a tip that they were travelling to the mainland to bring cocaine back to Vancouver Island.
The police followed and then stopped the vehicle on Sunday as it emerged from a ferry.
After searching the car, police say they went to the couple's home where they seized more cocaine and crack, for a total street value worth about $16,000.
A 35-year-old man and 39-year-old woman are under arrest and police have contacted the Ministry of Children and Family Development to care for the toddler.
Both accused face charges of possession for the purpose of trafficking drugs and will appear in court again later this year.