More than 20 trees will be removed from Flinders Street because of the unprecedented rain.
The trees have become unstable due to the severe weather.
Council crews will start work tomorrow to remove the trees and they will be taken off site to be mulched, reducing any inconvenience to CBD traders.
The planning for the replanting program has already commenced.
Improvements will be made to the planting foundations before any new tress go in.
Townsville Local Recovery and Resilience Group Chair Cr Les Walker said a city-wide clean up and recovery effort had already started.
"This is going to be a long process for our community to recover from such unprecedented rainfall," Cr Walker.
"All areas of our community received huge rainfall totals and that's why we are removing these trees in Flinders Street.
"The ground in many parts of the city is still drenched and Council crews will be monitoring if any trees fall around the community."
Local Councillor Ann-Maree Greaney said Council crews will do everything possible to minimise the impact on local businesses during this work.
"Council remains committed to greening the CBD but these trees need to be removed and improvements made before new ones are planted," Cr Greaney said.
"I'd like to encourage everyone to drop in to the CBD for a meal or some shopping to help our CBD traders get back to business as usual."
