Walkways on either side of the Water of the Leith, from the Leith St footbridge to Forth St, will be closed to the public for the next few months.
The closures will allow contractors to begin work on the next stage of the Leith flood protection scheme.
The council has let the construction contract to Lund South and the company will begin work in the next few days.
Council environmental engineering and natural hazards director Gavin Palmer said the work was being carried out over the summer to coincide with the university holidays so as to minimise disruption to vehicle and pedestrian traffic.
"Access to the construction zone is prohibited while the work is under way, and a parking area adjacent to the university commerce department building on Clyde St will be closed."
The Leith St footbridge would still be accessible during the work.
Weather permitting, it was expected the works would be completed by February-March next year before the risk of a flood event increased with the arrival of autumn, he said.
It was the latest in an eight-stage project to reduce flooding hazards for the central business district, including University of Otago property and facilities, while improving the area's aesthetic appeal and physical access to the water.
The Cumberland to Dundas Sts stage was completed earlier this year.
The works' design was the result of 12 months' "constructive discussions" between the council and the university, Dr Palmer said.
There were many elements to the work, which mainly involved removing the upper sections of the existing concrete walls on both sides of the channel between the Leith St footbridge and Clyde St and the true right bank between Clyde St and Forth St.
The lower sections of concrete wall would secure the edge of the river channel, while providing greater visual and physical access to the river bank, he said.
The river would be widened by excavating both banks between the Leith St footbridge and Clyde St and the true right bank between Clyde St and Forth St.
The works would not be fully effective in reducing flooding hazards until the other stages upstream were completed, he said.