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.
"The expectation was that Horizons would properly implement it and over time that would produce improvements in freshwater quality," Mr Taylor said.
He said all parties had been in discussions over the past few months but "in the end there is a gulf between us on what the council's responsibilities are".
The court will be asked to make a declaration on "legal questions" about the implementation of the plan in relation to Resource Management Act, the National Policy Statement on Freshwater Management and the One Plan.
"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," Mr Taylor said.
Fish & Game's Wellington regional manager Phil Teal said it didn't expect "radical change overnight" but "we did want a realistic approach which produced measurable improvement over time."
"Instead all that happened was existing practices being grand-parented and that just isn't acceptable."
Last year the Chronicle revealed many intensive farming operations in the region were being granted discretionary consents at up to three times the nitrogen leaching limit set out in the One Plan.
And earlier this year data obtained by the paper showed at least 40 per cent of farms which had a January 1, 2016 had not applied for resource consent by the deadline.
Today more than a quarter still have not.
Fish & Game New Zealand first called for a review of the council's implementation of the plan in October last year.