Plans to expand a quarry to within 50 metres of Brockadale Nature Reserve on the North Yorkshire-Wakefield district border, were approved earlier this month.
Hundreds of people, including many from the Pontefract area who enjoy the reserve, objected to the application.
The trust, which runs Brockadale, were also strongly opposed to the plans, citing the potentially devastating impact on animals and plants living on the site.
Now, in their first public statement on the matter since North Yorkshire County Council's planning committee approved the plans, the trust has praised those who fought the proposals.
The trust said: "We are very disappointed, as are many others, that the committee voted to approve the application, as it poses a serious threat to the reserve - a precious space for wildlife designated a Special Site of Scientific Interest (SSSI).
"We would like to take this opportunity to thank those in the local community who stood up for the future of Brockadale.
"Despite the outcome, we were so encouraged and inspired by your well-prepared and professional statements in support of our nature reserve.
"Now, more than ever, we need more people to speak up for nature."
The trust added that it would, "continue to protect Brockadale nature reserve as a sanctuary for wildlife and people alike."
Local Democracy Reporting Service