Lowering groundwater levels posed a risk of sea water intrusion, risked existing users groundwater take, and risked the health of the Kaimaumau Wetland, they said.
They then gave the green light to the 17 orchardists to plug in and take 2,060,655 cu/m annually from three aquifer zones, to water 600ha of avocado orchards.
Based on technical information from the applicant and (NRC) experts, "there is agreement the amount of recharge to the aquifer can comfortably sustain the proposed level of groundwater abstraction,'' the commissioners said.
The huge volume of water will be drawn from a deep shell bed layer of the aquifer, and several submitters expressed fears the fragile layer could be punctured or lowered too much.
The commissioners said an adaptive management strategy and staged build-up to taking the maximum volume would counter ''uncertainty about the magnitude of change that might occur".
The land and aquifer are inside the Kaimaumau Wetland catchment, which is classified as nationally significant.
Opposing the consent, the Department of Conservation (DoC) said the application was for a non-complying activity under the NRC's own Regional Water and Soil Plan.
The application used climate change data based on the previous 60 years. It did not include an ecological change assessment or demonstrate how adverse effects on the nationally significant wetland could be avoided, DoC said.
Yesterday a spokeswoman said DoC was considering whether to appeal the decision.
Local people had earlier voiced concerns about the proposed high volume draw.
In March, Far North group We Are Water spokeswoman Karen Nikora-Kerr said not only was "this huge amount of water" unnecessary, but potentially risked shallow bores and saltwater intrusion into the aquifer.
Notification of the consent applications was given to around 1000 neighbours in late October last year.
Of 57 submissions received, 42 opposed it, eight supported it and seven were neutral. They were heard over three days at Kaitāia.
Locals and environment groups have also complained of a lack of consultation, and the destruction of archaeological sites including middens and gardens, dune systems and other natural features during the orchards' development.
Nikora-Kerr earlier described the scale of the avocado expansion as ''mind-boggling''.
Fiona Furrell, from Northland Environmental Protection Society, said the consent amounted to ''wait and see if a worst-case scenario occurs, then try to do something about it.''
As well as fears of draining or contaminating the freshwater aquifer, the developments had already taken out an entire dune system, land had been excavated and flattened right up to a pa site and archaeological sites ''annihilated'', Furrell said.
Not considered an affected neighbour, the environmental protection group was not invited to submit to the water take application.
One of the water rights went to Ngai Takoto Trust whose chief executive Rangitane Marsden was unavailable for comment about the hapu's orchard development.
