Commuters face major delays of up to an hour across Victoria's transport system in coming weeks as upgrades, track maintenance and level crossing removals get underway.

Much of the work will take place during the school holidays and Easter long weekend.

The geotechnical works for the $11 billion Melbourne Metro Rail Tunnel have been completed, laying the groundwork - literally - for construction to begin.

City Square in the CBD will be surrounded by hoarding next month as work proceeds on the tunnel project.