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The two-stage $500,000 project requires a 3m channel to be excavated at the harbour entrance to bring a dredge into the harbour about March, timed to prevent the work spreading marine algae.
It will be the first time since late 2011 the harbour has been dredged.
In February 2012, the Otago Daily Times reported the council put aside $100,000 a year for dredging work in the past, but stopped the practice during the 2012-13 financial year.
The council has reinstated the practice.
In June the council set the budget for the initial dredging of Oamaru Harbour at $500,000 for the first year of the 2018-28 long-term plan, with subsequent dredging at $150,000 every second year from year three.