It asked for a five-year consent to take the water during summer months.
Objectors said the reason is "frivolous" and outside policies meant to ensure efficient use of New Zealand's water resource.
Mokau Marea chairman Hepi Haika said the marae had not been notified by either the applicant or NRC of the request for water.
Group manager regulatory services Collin Dall said that, as was standard practice, in April the NRC provided a copy of the application to Maori groups which had registered interests in the area to allow comment on cultural matters.
"The council determines the persons affected by a consent application in accordance with the relevant provisions of the Resource Management Act 1991,'' he said.
"Concerns expressed by persons on a particular application who are not determined by the council to be affected by the application cannot legally be treated as formal objections.''
A response was received from the Ngatiwai Trust, stating it had no concerns with the application, Mr Dall said.
Of the four objections it had received, the NRC deemed only downstream Helena Bay resident Rosie Stone counted as an "affected" party.
Ms Stone's own consent to take 3.5 cubic metres a day for stock would not be affected by the lodge's upstream take, the NRC said.
Three later objections, deemed informal by the NRC, came from Millan Ruka of Environment River Patrol Aotearoa, Mr Haika and Ngatiwai environment manager Hori Parata.
"None of [those] parties have identified anything that suggests they could have affected party status," an NRC report said.
Those objectors have refuted claims on the application that the stream was not used for food gathering, swimming and fishing, had no aesthetic value and was not significant to iwi.
Major earthworks before and during the development of Helena Bay Lodge had changed the stream's habitat but it remained significant to iwi, the objectors said.
There is a registered pa site on a mountain overlooking the stream and archaeological studies show the stream was a well-used path to the sea and gardens.
Mr Ruka said iwi values and history would have been explained had the questions been asked.
He said the proposed take from seven locations - with two figures given in the application, first 60cu m and later in the document 80cu m - was unsustainable.
The council had no flow data of its own on the stream and was using a measurement provided by the applicant, which Mr Dall said was common practice.
On February 17, NRC wrote to the applicant: "We don't have any information about flows in that area so your best guess is probably as good as it gets."
The objectors claim NRC had not carried out due diligence, had not suggested the applicant get expert advice and had given beneficial guidance to that party but not to Ms Stone and the other objectors.
The application timeframe was extended to June 20 to give Department of Conservation (DoC) time to comment, but DoC had not responded
The NRC expected to make its decision next week.
The application was lodged by Neil McFarlane, a Helena Bay Holdings Ltd director.
The lodge, 40 minutes northeast of Whangarei, was built by one of the world's richest men, Russian steel billionaire Alexander Abramov.
Several years in construction, it opened late last year to take 10 guests at a time, with a villa suite in summer months advertised at $3850 a night for a double occupancy.
