The Government's Action for Healthy Waterways package will go some way toward improving water quality but also "significantly" affect the business of some farmers and cost Horizons region ratepayers.

The package, announced on August 5, comes into effect in stages, starting on September 3.

It sets new rules for fish passage and stock exclusion, caps nitrogen fertiliser use and stops some intensive winter grazing practices.

The package puts the health and wellbeing of water as a first priority, with the essential needs of people second. Protecting threatened species and providing places for kai gathering join ecosystem health and human recreational health as values.

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Regional councils will have a key role in making the package work, Horizons chairwoman Rachel Keedwell said. Horizons will now look at how to implement it and whether it will affect proposed changes to its One Plan.

Adding it into the council's workload will be a cost for ratepayers, Horizons chief executive Michael McCartney said.

"Resourcing to deliver revised regional plans, and the demand on ratepayers to fund extensive policy, compliance and monitoring requirements will be high."

Horizons already did much of this work, he said, but it will need to do more.

The package will make Farm Environment Plans and fencing some waterways compulsory during the next five years, and it will limit farm intensification.

The council will be informing landowners about it, but also asks them to be proactive.

"If I was one of the farmers that are going to need to come into this regulatory framework I would be looking at steps I could take to get my nutrient leaching down," Keedwell said.

The 190kg cap on farms' nitrogen fertiliser use will be a real challenge for some farmers, DairyNZ chief executive Dr Tim Mackle said. He was glad farmers will be given time to reach that.

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However, he said, Government's limits to nitrogen toxicity in waterways have been placed too high. He advocated allowing for lower levels of aquatic biodiversity in very productive and highly modified catchments.

The package stops short of setting limits on dissolved nitrogen and phosphorous in waterways, which disappointed Forest & Bird freshwater advocate Tom Kay.

He said the package was good but more could be done, given most of New Zealand's lowland rivers are unsafe for swimming and nearly half of monitored lakes have a nutrient overload.