One water issue remains unresolved but Horizons Regional Council is to begin a new catchment-by-catchment consultation on water quality, strategy manager Nic Peet says.

Under the Government's National Policy Statement for Freshwater Management councils nationwide must engage with residents and set water quality goals by 2025.

At the same time Horizons is grappling with how it gives consent for intensive farming.

Last year Fish & Game and the Environmental Defence Society took it to court over granting too many intensive farming consents, to the detriment of water quality.

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The Environment Court found the council had acted unlawfully, and it is now deciding how to react. Staff have had an informal "meeting of minds" with planners from the environment groups.

They are preparing a report about possible responses. If a quick and simple response is possible then farmers could know in December, at the earliest.

The national policy statement sets a bottom line for E. coli, nitrogen, phosphorus and other pollutants in freshwater.

But Peet said people in catchments may be more ambitious.

"People want as good a water quality as possible, and healthy, resilient communities alongside."

How ambitious they are could depend on whether there are towns discharging treated wastewater into their catchment, or whether there is intensive farming or very erodible soil.

Council staff have started talking to iwi, councils, farmers and environment groups in some catchments, about how the consultation should be done.

When people have decided what they want to aim for, the health of their waterways will be measured and they can decide how to make improvements. It will be a decade-long process, Peet said.

The Whanganui and Whangaehu catchments are likely to be some of the last consulted in the region, because both have relatively new Treaty of Waitangi settlements.

"We aren't starting that process in the Whanganui catchment until we have had the right level of dialogue with Ngā Tangata Tiaki, given the Te Awa Tupua settlement."