Mr Taylor said Horizons should feel "a little chastened" because the court was quite critical of its procedures.
Horizons chairman Bruce Gordon has maintained the council is improving water quality, but not fast enough for the groups. The judgement said there was no way the council could know this.
"The council cannot possibly be confident that water quality is being maintained or improved."
Horizons will have to do things differently, and Mr Gordon said that would make resource consents longer, costly and more involved. Mr Carlyon agrees with that, because an assessment of environmental effect will be needed.
"It is both unlawful and diabolically poor practice not to have one."
Horizons has issued about 200 consents under the One Plan, with hundreds still to come.
Mr Gordon said the council would now suspend issuing new consents, including those already in the pipeline, for 12 weeks, while it considers how to continue. Mr Carlyon said that should be obvious.
"Any competent planner should be able to process a consent in line with that plan."
The council is not planning to change consents issued so far. But Mr Carlyon and Fish and Game CEO Bryce Johnson say they must be reviewed, and it will be difficult.
"Farmers have invested millions of dollars on the back of really poor advice. Some of the consents are for up to 20 years for [nitrogen leaching rates] far too high."
Mr Taylor has asked Horizons chief executive Michael McCartney for a meeting to talk about what's next.
Federated Farmers Manawatu/Rangitikei president James Stewart said Horizons had worked hard to implement the plan in a way that would not put farmers out of business and would improve water quality as needed. He urged farmers to keep up their environmental efforts, despite the uncertainty the judgement brings.
The court's judgement is also expected to have far reaching consequences for other regional councils.