The Louis-Hippolyte Lafontaine Bridge–Tunnel opened in 1967 and is beginning to show its age.
Transport Quebec says decades of salt and water have been eating away at the tunnel.
The provincial government is now accepting bids from companies to control the rust.
"We will be applying a special coat to protect the reinforcing steel and also the concrete walls and ceiling," said Transport Quebec spokesperson Sarah Bensadoun.
She said the rust does not come as a surprise and that drivers shouldn't worry.
"The structure is aging but I do want to mention that the structural integrity is not compromised. This is a preventive measure that we are doing," said Bensadoun.
The government is expecting the repairs to cost between $1 and $5 million.
The work means two out of three lanes will be shut down, but the work will only be done at night.
Bensadoun said the job should be completed before the end of the summer.