Water quality management in Whanganui and Manawatu, and whether the regional council is implementing its own rules properly, is set to be argued in court.
At issue is Horizons Regional Council's One Plan, which was adopted in 2014 as a "one-stop shop" resource management planning document.
But the Environmental Defence Society (EDS), and Fish and Game NZ say they are frustrated at how Horizons is implementing the plan.
The two groups say they will be filing proceedings in the Environment Court this week challenging the council.
EDS chief executive Gary Taylor says there is concern that Horizons hasn't been following the plan lawfully, particularly when dealing with resource consent applications for intensive farming and dairy conversions.
"The One Plan sets environmental limits for freshwater and these have been thoroughly scrutinised through various hearing and appeal court processes," he said.
"The expectation was that Horizons would properly implement it and, over time, that would produce improvements in freshwater quality."
Mr Taylor said the two groups had had discussions with Horizons staff in recent months, but there was a gulf between the parties over the council's responsibilities are.
"In short, we are not convinced the One Plan's freshwater quality limits will be achieved given the way the consenting regime is presently being managed."