Cory Breton and Iuliana Triscaru could be heard calling out and pleading for their lives as the box was pushed into the water before they died.
Tuhirangi-Thomas Tahiata, 28, denies murdering the pair at Scrubby Creek in Kingston on January 24, 2016.
But prosecutor David Meredith says he drove the ute that carried them from the home on Jeurs Street to the waterway.
Tahiata is alleged to have also handed one of his six co-accused a claw hammer so he could smash holes in the box before it was pushed into the water.
“This is a breathtakingly evil act,” Mr Meredith told the Brisbane Supreme Court in his opening address.
The court heard Mr Breton and Ms Triscaru were lured to the two-storey unit about midday after Mr Breton was seen with a photo of an alleged drug dealer on his mobile phone by associates.
There they were allegedly assaulted and tied up before being forced into the box.
Tahiata and one of his co-accused allegedly then drove Tahiata’s Toyota Hilux ute with the toolbox on the back to a nearby quarry in the early evening but the gates were locked.
It was then that Tahiata’s co-accused suggested they take it to the creek.
Tahiata initially denied he was involved in the killings to detectives but on February 10 he confessed and took officers to the site, Mr Meredith said.
The following day, police pulled the box with Mr Breton and Ms Triscaru’s decomposing inside from the water using a mobile crane.
The court heard the pair either drowned or suffocated.
After he was charged Tahiata changed his tune saying he wasn’t “going to take the blame for what other people had done”.
The trial continues.