Five other people were injured, including a "brave" police officer who had hypothermia after jumping off the Maungatapu Bridge to rescue a passenger in the van.
A body was located by police divers inside the submerged van's wreckage late this morning.
The van was winched back up onto the bridge by a vehicle-mounted crane.
It took about 90 minutes for the van to be pulled up out of the water.
The dead man's family are in the process of being notified and a formal identification will need to take place, police said in a statement.
"The man will not be named until this process is complete.''
The van that plunged into Tauranga Harbour belonged to local electrical services firm, Amp'T Electrical.
Company director Simon Fannin said he was about to speak to the dead employee's partner and did not wish to comment.
He referred media enquiries to the company owner, who was unavailable for comment when APNZ contacted his depot this afternoon.
The Mangatapu Bridge is now open to all traffic, police said.
