Legal proceedings are being filed against Horizons Regional Council over the implementation of its One Plan.
The council will be challenged in the Environment Court by the Environmental Defence Society and Fish & Game.
"We are concerned Horizons hasn't been implementing its regional plan lawfully, particularly when dealing with resource consent applications for intensive farming and dairy conversions," EDS chief executive Gary Taylor said.
The One Plan was adopted by Horizons in 2014 after a decade of planning, hearings and legal challenges.
It put limits on nitrogen leaching by intensive farm operations, namely dairy farming, commercial horticulture, cropping and intensive sheep and beef farming and required existing operations in targeted water management areas to apply for resource consent.