A Land and Water Commission should be created to stop further damage to New Zealand's waterways, a top-level forum says.

In its new report, the Land and Water Forum called for a national body to oversee measures to protect and manage the country's lakes and rivers.

It also sought urgent action to save those most threatened, and for the vexed issue of iwi rights and interests to be finally resolved.

"Local authorities and courts have been left to interpret and implement the emerging framework without any effective oversight, which has resulted in slowed and inconsistent implementation," said the forum's chair, Dr Hugh Logan.

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"More should be done, and a concerted effort at national level will be required to push forward robust and co-ordinated change in both urban and rural water management."

The forum - a group bringing together farmers, environmentalists, scientists, iwi and other sector groups - set out nearly 40 recommendations after the Government asked it for advice on how to stop waterway degradation.

Around towns and cities, the forum advocated stronger measures to address urban impacts on water quality.

That included regulations to stop pollution caused by development, and creating standard consent requirements for stormwater and wastewater management so rules around the country were the same.

It also recommended stronger action to protect wetlands and special water bodies, and the closure of loopholes in the Resource Management Act (RMA) and the National Policy Statement on Freshwater Management (NPS).

Much of the just-released advice focused on nitrogen, a nutrient that can fuel algal blooms in waterways and which has become a bigger pollutant as the dairy industry has expanded and intensified.

The forum suggested a staged process for addressing the allocation of nitrogen discharges, which involved limits on nitrogen in water bodies and a short-term plan that allowed for a shift away from present practices.

The short-term plan would focus on over-allocated or at-risk catchments, manage down high dischargers and allow some flexibility for low dischargers, all with an overall environmental limit for the affected catchment, the forum said.

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It advised against using certificates of compliance to avoid addressing nitrogen problems, and backed extra support for councils faced with situations where too many issued consents were causing problems.

But ultimately, the forum couldn't reach agreement on the allocation of nutrient discharge rights in polluted catchments.

Another step was that at sectoral good management practice - effectively a social licence to operate - be codified and made mandatory for those whose activities could affect waterways.

In the long-term, the forum said the prickly issue of iwi rights and interests should be finally addressed, and that the system eventually adapted should ensure land was used according to its ability to absorb nutrient discharges.

"Our message to Government is that councils and sector groups need strong central government leadership to address the complex issue of water quality, but what we have recommended will be a significant step forward in holding the line," Logan said.

While New Zealand had made some progress with reforms over recent years, more improvements were needed, he said.

Environment Minister David Parker said the Government would act on some of the forum's recommendations "immediately", while the others would be considered as part of its work programmes.

The Government has been looking at bringing in a new NPS that would give councils a fresh set of bottom-line rules when setting their own policy.

While regional councils held much information about the state of catchments in both urban and rural parts of each region, there was currently no coherent national picture, and a joint water directorate sitting across the ministries of environment and primary industries.

"As we look at what's happening in these catchments and what needs to be done, we will work closely with the primary sector, Maori and other interested groups," Parker said.

Parker has indicated the new NPS would remove farming intensity - blamed for driving pollution in rural waterways - as a "permitted activity", while setting new nutrient levels.

He has also ruled out direct subsidies for land-use change - instead, that could be enabled through new technologies that the Government was willing to subsidise to bring forward.

Labour - whose coalition agreement with NZ First vaguely referenced "higher water quality standards for urban and rural using measurements which take into account seasonal differences" - had also pledged in the election to make all rivers and lakes to be swimmable, with extended quality standards.

Environmental Defence Society chief executive Gary Taylor said the forum's fifth report also spelt out a critical role for Parker by recommending the use of prohibited activity status or moratoria to "stop the rot" in catchments where water quality was dire and councils weren't acting fast enough.

"In some catchments this might mean no more cows until plans are set; in others it might be a short term stop to subdivision."

Taylor noted the report scantly addressed consents for intensifcation - something his group expected would be required in most catchments.

"Without this it is extremely difficult for councils to account for and control the amount of contaminants entering waterways."

But Federated Farmers' representative on the forum, Chris Allen, argued the issue wasn't just an agricultural one.

"No-one in New Zealand is in a position to throw stones when it comes to water quality," he said.

"Every community has its fair share of glass houses - both urban and rural."

Five big recommendations

• Establish a Land and Water Commission to provide national oversight.

• Identify at-risk waterways and make sure there are plans in place to stop further damage.

• Require good management practice by all sectors.

• Draw up a staged process for addressing the allocation of nitrogen discharges.

• Address iwi rights and interests.