"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.