The judgement directs the council to assess environmental effects, including cumulative ones, when considering consents.
It must stick to One Plan and Resource Management Act requirements, and not take resolutions by councillors or financial implications for farmers into consideration.
Horizons Chairman Bruce Gordon has maintained the council is improving water quality, despite the judgement stating there was no way the council could know this.
"We respect that we may not have got it completely right, however no one has said that we're not on the right path when it comes to water quality improvement," he said.
"Some groups have simply indicated that they would like to see faster implementation."
A Horizons media release this week said there is a significant monitoring programme across the region, and that 58 per cent of the 36 sites monitored for total oxidised nitrogen show improvement while none are in decline.
However, Mr Taylor said Horizons should feel "a little chastened" because the court was quite critical of its procedures.
In Horowhenua, Horizons had previously said that a number of waterway sites showed "signs of pressure," and reducing run-off through stock exclusion was one way it was endeavouring to improve water quality in the district.
There were requirements in place for dairy cattle to be excluded from waterways, but this is not always the case for beef cattle.
A Horowhenua Chronicle story last month drew national debate when cows were photographed cooling off in the river near Gladstone Reserve on the Ohau River, not only a popular swimming spot, but the source of Levin's drinking water.
Horizons said at the time that there were no legislative requirements for beef cattle to be excluded from Ohau River, but they would work to "encourage" the farmer to stop the practice.
Regarding consents for intensive farming, the council is now facing having to do things differently, something Mr Gordon said would make resource consents longer, costly and more involved. Assessments of environmental effect will be required.
Horizons has issued about 200 consents under the One Plan, with hundreds still to come.
The council is not planning to change consents issued so far, but Fish & Game CEO Bryce Johnson said they must be reviewed, and it will be difficult.
He said some of the consents last for up to 20 years with nitrogen leaching rates that are far too high.
Mr Taylor has asked Horizons chief executive Michael McCartney for a meeting to talk about the next step.
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.
Horizons strategy and regulation manager Dr Nic Peet said the council had sought to appropriately apply its Plan in line with the Resource Management Act at all times.
"Like any new piece of legislation it's met some challenges along the way, the court process will help inform these challenges," he said.
The court's judgement is also expected to have far reaching consequences for other regional councils.
