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Auckland Council's regulatory compliance manager Steve Pearce confirmed there were concerns regarding the water run-off sweeping debris and contaminants into the harbour.
About 16 million litres of water have been used so far to fight the blaze - and some of this will enter the harbour via the stormwater network.
Firefighters are pumping an estimated 200 litres of water per second on the blaze.
Watercare's Ponsonby and Auckland Domain reservoirs have been providing around 200 litres of water a second more than normal. This has not affected the rest of the city's water supply.
Craig McIlroy, who heads council's Healthy Waters division, said between half and three-quarters of the water used to fight the fire will be released into the atmosphere in the form of steam.
The remaining road run-off enters the stormwater system with cesspits for solids to drop out. A "pretty small volume" of polluted water will enter the harbour, he said.
McIlroy said the environmental impact of the fire for the harbour would be short-term, saying after one or two tidal cycles the contaminated water would go out into the wider channels.
Pearce said the Resource Management Act has a provision during emergency situations such as the SkyCity fire which allows for run-off from fire-fighting to occur.
"It is a balance to ensure there is minimal impact on our waterways while also ensuring that emergency services can prioritise the response.
"Fire and Emergency New Zealand work hard to ensure that this run-off is minimised. Auckland Council and Watercare will be monitoring this as the incident continues," he said.
A mayoral spokeswoman said in an emergency situation such as this, containing the fire is the first priority.
"In these circumstances, we are advised that it isn't possible or practical to pond and cleanse the water. We are also advised that any run-off that makes its way into the stormwater system will be very diluted," she said.