Fish and Game is taking the Southland District Council to the Environment Court over plans to build a cycleway along the Oreti River.
Resource consents for the project were granted in February.
Southland Fish and Game regional manager Maurice Rodway said the effects of the development on the habitat and character of the Oreti Valley would be significant.
"It's the building and all the structures that are needed - the bridges, the culverts, the boardwalks and ... to maintain all of those things over the years will have quite a big impact on this valley."
Mr Rodway said paperwork to appeal the decision had been filed in the Environment Court.
However, Fish and Game would like to talk to the Southland District Council about other possible routes or alternatives, he said.