Our authorities must do better in managing New Zealand's precious water resources, a new report from the Auditor-General has found.

A wide-ranging review of the way councils and the Government oversee our water – including drinking water, wastewater, allocation and river quality – has found that public agencies need to be much more strategic and collaborative.

Auditor-General John Ryan wrote that, when his office set out to look at the way water was being managed in New Zealand, it expected to find clear national strategies and work programmes, strong systems for gathering information, good engagement with the public – especially Maori – and resourcing that reflected the scale of the issues.

"We found that, although much good work is being done, all of these elements were not in place," Ryan said.

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"What we saw were public organisations trying to do the right thing while working with the resources they have, within the limits of their own roles and responsibilities, and in a context of increasing complexity and uncertainty."

What wasn't seen, he said, was clear agreement across central and local government over goals and priorities.

"The lack of clarity about what the issues are, how to address them, and who will deliver programmes of work increases the risk that public organisations are not directing their efforts towards the same outcomes," he said.

"It also means that some organisations might carry out work that conflicts with or duplicates that of other organisations, and that investment and policy decisions are not targeted to address the greatest risks or achieve the greatest benefits."

Public agencies were sometimes making decisions without reliable information about water resources – a finding that Parliamentary Commissioner for the Environment Simon Upton also stressed when commenting on glaring data gaps in our reporting systems.

"For some time, we have reported that public organisations need better information about the condition and performance of assets, including water, wastewater and stormwater assets," Ryan said.

"Because of gaps in this information, those responsible for managing the assets that deliver water-related services are often limited in their ability to make well-informed decisions.

"It also limits the ability to have informed conversations with communities about the risks they are willing to accept, such as the level of flood risk they might be exposed to."

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The Government is part-way through a major reform with its Essential Freshwater programme.

They include new environmental standards that would effectively put the brakes on further intensification of dairy farms; a requirement for farmers to have "farm plans" by 2025 and more stringent rules around fencing and nitrogen loss, with some catchments facing having to cut rates by as much as 80 per cent over the next few years.

Councils would have to put the health and wellbeing of water first in decision-making, adopt tougher rules for wastewater discharges, use more monitoring indicators, and ensure swimming spots were at higher standards over summer.

A separate series of reforms, emanating from the cross-agency Three Waters Review, has also led the Government to create a new regulator for drinking water.