Local mana whenua, Ngāi Tai Ki Tāmaki, said the discharge was a "direct insult to their mana".
High levels of E. coli also posed a potential health risk to people using the stream.
Auckland Council filed six charges under the Resource Management Act against Formosa (NZ) Ltd, with the company pleading guilty to all counts.
Environment Court Judge David Kirkpatrick has now sentenced Formosa to pay $86,250.
He said while he did not think the company intended to discharge waste to the creek, he did find that the problems with the system were not given priority.
"Accordingly, the offending was extremely careless," he said.
"The nature of the discharge made any amount of it a serious matter."
Auckland Mayor Phil Goff said he was pleased to see the company fined.
"This pollution resulted from repeated acts of negligence and caused serious damage to Auckland's natural environment," he said.
"The offender was made aware of the problems, but deliberately chose to ignore them.
"Had they chosen to engage with the council when asked, the problems could have been resolved and further action avoided, but given their indifference a punitive fine is entirely appropriate.
"I hope this fine will act as a deterrent to those who would choose to pollute Auckland's waterways, especially given the significant resources we are investing to improve water quality across the region."
Council regulatory committee chairwoman Linda Cooper said Aucklanders placed great value on the natural environment, and it was important those who breached environmental standards and polluted waterways were held accountable.
Regulatory compliance manager Steve Pearce said Formosa knew about the wastewater treatment problems, but ignored several abatement and infringement notices and failed to take steps to address the issues.
"This kind of negligent pollution is completely unacceptable, but also completely avoidable.
"If the company had acted when we first discussed it with them, the situation could have been remedied.
"Instead it has let the cost of fixing the problem early lead to what is a bigger financial penalty.
"We will not hesitate to take action against anyone else operating with such careless disregard for the law and the environment."
An entity established by the NZ Super Fund and the owner of one of New Zealand's largest construction businesses, Russell Property Group, bought the resort this year.
The waste system was fixed prior to the sale, council said.
