The changes are due to V/Line annual maintenance works.
Coaches are replacing all trains between Southern Cross, Bendigo and Echuca.
Passengers are reminded to add 60 minutes of travel time for their journey.
From Monday, March 9, temporary speed restrictions will be in place on parts of the Bendigo and Echuca lines, following major works.
During this time, trains will run at slower than normal speeds between Bendigo, Echuca and Sunbury to allow the tracks to bed down.
Restrictions will be in place until Sunday, March 28.
There will be changes to arrival and departure times, so passengers are advised to plan ahead and check the temporary train timetable or journey planner before they travel.
All Bendigo and Echuca Hill trains to the city will depart stations up to three minutes earlier.
The weekday 7.23am Echuca to Southern Cross train will arrive at Southern Cross 20 minutes later.
The weekend 7.25am Echuca to Southern Cross train will arrive at Southern Cross 10 minutes later.
All trains travelling towards Bendigo and Echuca will arrive up to five minutes later.
Passengers are advised to download the temporary timetable.