Residents say the granting of a discharge licence to Dairygold will result in millions of litres of effluent being pumped into the water at Rathcoursey.
Locals say the move will lead to widespread pollution.
Dairygold say their new €120 million facility 14 kilometres away from the sea in Mogeely will employ 67 people and will provide a Brexit-proof market for milk from Cork dairy farmers.
They also say they are committed to adhering to the most stringent standards set down by the Environmental Protection Agency and that water quality is a key element of their agenda.
Speaking to RedFM News, Eddie English from SailCork says pumping effluent into Cork Harbour make no sense:
