Horizons has suspended issuing consents for three months, until it decides how to react. At present it can't see any way around simply refusing consent to most farmers who apply for it. Ms Keedwell said one immediate possibility would be to give shorter consents.
She would like a meeting of experts, to look for other possibilities, because farmers given consents in the Tararua catchment may find they are farming illegally. Most Rangitikei farmers can meet the table.
The council is also struggling to understand the issue.
"We have lawyers talking lawyer language and we are trying to get that broken down into our language. It's a hell of a mess at the moment," Mr Gordon said.
Horizons has to have a process for considering consents in place by August 9. Any perception that the council is not swiftly implementing its plan lays it open to further legal challenge.
"We do have to get on and do the stuff. It might be processing [consents] in a way that people can't live with. Then they will appeal, and we will be back in court again," Mr Gordon said.
Environmental Defence Society (EDS) chief executive Gary Taylor said the position Horizons advanced to the court was not accepted, and the council would have to adjust.
"They now need to implement the court's findings. That's going to require some contortion, and a pretty fundamental re-think."
In April the council was not minded to review the 200 consents already issued. But Fish & Game chief executive Bryce Johnson said that had to happen.
Mr Gordon said the consents would not be reviewed, because the court had said they were out of scope. He rejects the court's finding that some farmers have been granted the ability to leach a lot, limiting options for others.
Ms Keedwell said Fish & Game or any individual can ask for a judicial review of consents already granted.
"If that happens the individual farmer could be embroiled in court action, through no fault of their own."
The Environment Court said an assessment of environmental effects (AEE) is essential in any consent for intensive farming. Getting an AEE makes the consent process longer, more costly and more complex - but it ensures nutrient leaching stays within limits.
Horizons staff fear the reaction of farmers to lengthier and costlier consents. Ms Keedwell said some could be put out of business, which would destroy the rapport the council has been building with the community.
Mr Taylor said people would have to get used to the more complex consents, and it is Horizons' responsibility to implement its plan.
"We are transitioning as a country to a greater awareness of a need for limits, especially for water quality. That's going to require some changes in the way people have done things."
Since the court's declarations Fish & Game and EDS have written to Horizons, outlining they changes they want to see.
Horizons councillors would like to meet with the two groups. Ms Keedwell said it would be better for officers to meet, because they are the experts in nutrient management.
She's frustrated by the situation, and the way it has limited progress the council could be making in reducing nutrient leaching. The current uncertainty would be putting farmers off taking any action, she said.
"If we had done a better job of implementing the plan straight up we wouldn't have been taken to court or forced to implement the plan as it is now, with a huge amount of scrutiny."