Auckland Council and DoC sought costs for both legal actions, submitting arguments put forward were "without substance" and their case "poorly presented".
In a decision on the first costs application Environment Judge Melanie Harland said the court agreed.
"The applicants did not provide the necessary admissible proof to support their case about adverse effects," the decision read.
She ordered the trust to pay nearly $20,000 to DoC - about a third of its costs, and nearly $23,000 to the council - about half of its total costs.
The council and DoC sought similar amounts again for the second application, which the judge ruled excessive but still ordered the trust to pay them each $5000.
The council approached the trust several times through 2020 about its payment of $27,912.96, but said it never received a response.
Subsequently, the council applied in February to put the charitable trust into liquidation.
Trust organiser Tricia Cheel said this would likely be the end of the "community action group", established in 1990, and predominantly concerned with chemicals in the environment.
"I am disgusted. This is what they do to the opposition. If we can get legal advice we will be challenging this.
"But we are not a revenue-gathering entity, we relied on donations for the legal challenges - this will likely destroy us."
In the court's first costs decision, Harland said most of the evidence filed was "opinion but not expert evidence", or there was insufficient information about the context to the alleged adverse effects or historical events.
The court took into account the view of the trust that it represented a view of some members of the community about the use of 1080 for pest control.
"However, it is just that - one view," the decision read.
That view was "comprehensively met" by the evidence from the council, DoC and the Public Health Service, which arguably also represented the public interest.
The arguments advanced by Friends of Sherwood were "legally without substance and the evidence about potentially adverse effects was evidentially problematic".
The judge also acknowledged the costs of the council and DoC were met by the public.
"Because this case concerned an application for interim enforcement orders which was required to be dealt with as a matter of priority, it was incumbent upon Friends of Sherwood to present an evidentially sound and legally sustainable case to succeed.
"For the reasons we have expressed above, it fell well short of the mark in this regard."
Asked about the fact ratepayers and taxpayers were still owed nearly $50,000, Cheel said it was unfair they were made to pay costs, given they were raising valid concerns about 1080 that were in the public interest.
"The case had merit, the court just decided not to listen.
"After 30 years we have done nothing but try make our neighbourhood a better place."
The Environment Court declined in both cases the council's application for costs from the Ngāti Paoa Trust Board, a joint applicant in the case but which was primarily concerned about lack of consultation as mana whenua.
The operation went ahead over September and October, and involved dropping sodium fluoroacetate (1080) by helicopter to 30,501ha across the ranges.
The Auckland Regional Public Health Service had developed various safety measures for the drop.
The council and DoC planned the 1080 drop to reduce pest numbers and maintain the natural habitat of the Hūnua Ranges in an area known as Kohukohunui. Pest levels had risen again after a successful 2015 operation.
A few months after the drop, the council reported the operation had reduced pest numbers to their "lowest-ever" levels, and led to a doubling of kōkako breeding pairs.
Auckland Council's application is to be heard before the High Court at Auckland on April 14.
