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The Avon River has become an outlet for sewage and will be contaminated for some time, officials say.
Signs along the city's usually pristine river warn people not to take water, or let pets go in.
The river is the city's rowing base, is popular with kakayers and whitebaiters.
City officials saidthe pollution was inevitable because of the damage caused by the earthquake to sewer pipes.
Areas around the river have been amongst the worst hit.
For more news on the Canterbury region visit the starcanterbury website.
