Anna Boyle, 28, and Aaron Johnson, 27, both of Woodinville, appeared in court Monday, the Everett Herald reported.
Both are charged with unlawful imprisonment, while Boyle also faces drug charges.
The couple have been held in the Snohomish County Jail in lieu of $25,000 bail each since their arrest Sept. 21, KCPQ-TV in Seattle reported.
A Washington State Patrol trooper pulled Boyle over for speeding, police said. The trooper said the back seat was full of items such as snow boards and that he found drugs in a roadside search.
During the search, the trooper heard noises from the trunk and discovered a girl, 8, and two boys, 5 and 7, along with the dog. Boyle allegedly said the children climbed into the trunk from the back seat of the car.
"There's absolutely no way those three kids would have been able to go from that back seat into the trunk," Trooper Kenneth Leary said. "There was no room for those three kids and a dog."
The children are now in the care of child protective services.