It stops council officially awarding the contract to build the pool until October, but preparatory earthworks and the resource consent process is allowed to continue.
Martin Williams, lawyer for the Society, said the work which could be done by the council during the injunction is essentially reversible.
"This was vital from the society's point of view to ensure that the horse hasn't bolted and work progressed to far before we get a final judgment from the court."
He said preparatory earthworks on the Prebensen Dr site would be needed for any form of development on that land, whether or not the pool complex goes ahead.
A spokesperson for Napier City Council said in practice, the agreement allowed planned work to continue on the pool and the evaluation of tenders received and acceptance of the preferred tenderer by council would proceed.
"NCC has agreed that a contract with a successful tenderer will not be entered into until after a decision is released on the full hearing for the legal challenge, which will be held on Monday 30 September."
If NCC succeeds in its defence, the new council, which is due to be voted in 10 days after the end of the court case, would not have to sign off on the new pool.
CEO Wayne Jack said being able to continue with preparatory work while awaiting the court case ensured cost and time savings.
"Construction costs are increasing at a rate of $3000 to $4000 per day."
The new pool has proved controversial both within the council and the community.
It was orginially consulted on during the councils Long Term Plan process, with 51 per cent of submitters in favour of the $41.3 million new pool.
49 per cent of submitters were in favour of upgrading the aquatic centre site at Onekawa, at a cost of $20.2 million.
The Long Term Plan, which included the new pool complex, passed 8 votes to 5.
In October 2018, council was presented with a petition with over 7000 signatures, asking for Council to save the Onekawa site.
In December six councillors called for an extraordinary meeting of council, asking for the pool to be re-consulted on, which lost 7 votes to 6.
In April this year, council agreed to the conditions of the tender, with the original vote 6-6, giving acting Mayor Faye White the deciding vote.
The tender process closed earlier this month.
The court case will be heard over three days in the Wellington High Court, from September 30 to October 2.