Karl Lilgert was charged in 2010 with criminal negligence in the deaths of Gerald Foisy and his common-law wife, Shirley Rosette.
Lilgert was the navigating officer on the Queen of the North when it sank March 22, 2006, after crashing into Gil Island off the northwest coast of British Columbia, about 140 kilometres south of Prince Rupert.
He was in court in Vancouver in Wednesday to enter a plea and for jury selection for the trial which will begin later this month.
Outside the court Lilgert's lawyer, Glen Orris, said he did not believe his client's actions amounted to criminal negligence.
"There is no issue with respect to his involvement. The question is really whether it's criminally negligent. We say it is not," said Orris.
A Transportation Safety Board investigation into the sinking determined Lilgert was on the bridge of the ferry with quartermaster Karen Bricker the night it sunk.
The pair had recently ended a relationship and it was their first shift alone together since the breakup. The report said the pair failed to make a crucial course correction and navigational warning systems were turned off.
Lilgert and Bricker were fired by BC Ferries after the sinking, but Lilgert was the only person ever charged in the incident.
The vessel's captain, Colin Henthorne, who was not on the bridge at the time of the incident, also lost his job over the sinking.Foisy and Rosette were the only people aboard the vessel who didn't survive — out of a total 101 passengers and crew. They are believed to have gone down with the ship, but their bodies were never found.