Judge Jeff Smith said the court agreed the existing environment around the yacht club was highly modified, with houses, reclamations, jetties, seawall, an extensive sealed car park and a motorcamp.
But large areas of the tidal estuary were natural. They were used by wading and migratory birds and the salt marsh was an environment for the rare banded rail.
There was no doubt the marina would have an effect on the bird habitat but on the other hand the breakwater would discourage pedestrian intrusion and replenishment of a beach would serve as an inter-tidal roost.
A condition of consent would be that construction be timed to limit interruption of bird feeding and breeding.
A further condition would be that the Auckland Council receive $10,000 to improve the bird roost area.
Club commodore Phil Brooker said the decision was welcomed after six years and $1.4 million in spending.
For Save our Sandspit, Michael Taplin said the interim decision was disappointing.
"But we accept it and are working on negotiating a robust set of conditions that will protect the interest, as best we can, of the community and the environment - what there is left of it."