Swimming at the Oroua river in Awahuri in Manawatu.

Most of New Zealand's native freshwater species are at risk of extinction as water quality faces "serious pressures", a Government report says.

Threats to native species were one particularly concerning aspect amid an overall decline in freshwater quality, determined in a joint report by the Ministry for the Environment and Statistics New Zealand.

The report added to mounting evidence that freshwater quality will get worse unless fundamental changes are made.

The report, titled Our fresh water environment 2017, found nearly three quarters of native freshwater fish species are threatened by or at risk of extinction, as well as a third of native freshwater invertebrates and a third of native freshwater plants.

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The report, part of the State of the Environment reporting series, measured water quality, quantity, biodiversity and cultural health. It found problems in all categories.

SUPPLIED The longfin eel is at risk of extinction.

It found nitrogen levels were worsening at more than half of the measured sites. Nitrogen levels were worst at urban sites, but were declining significantly in pastoral areas.

The decline in pastoral areas coincided with an increase intensive agriculture. Nitrogen leaching from agriculture had increased by 29 per cent since 1990, it said. The main source was livestock urine.

Urban waterways had the worst overall water quality, degraded by stormwater and wastewater. About a quarter of wastewater assets are more than 50 years old.

Water quality overall was a mixed picture, but it was clear some trends were going the wrong way.

"Urban water is the most polluted, but the trends are worse in pastoral areas," said Secretary for the Environment Vicky Robertson.

"Very high levels of nitrogen can be a problem as they can make water toxic for species and unsafe for drinking.

"We aren't seeing this playing out yet, but as nitrogen levels are trending the wrong way, this is something we need to address."

While urban areas had the worst water quality, they covered less than 1 per cent of land but were home to 87 per cent of the population.

Pastoral areas covered 40 per cent of land use.

While it was difficult to make an overall assessment due to variation between areas, it was clear there were fairly widespread freshwater issues.

"[Thursday's] report confirms our fresh water environment faces a number of serious challenges," Government statistician Liz MacPherson said.

Like other recent freshwater reports, it concluded changes would need to be made if freshwater was to improve.

"New Zealand's population and agriculture-based economy are growing, and it is expected that high-intensity agriculture and urbanisation will continue to expand to new areas, potentially affecting water quality in more water bodies," the report said.

SWIMMABILITY AND BIODIVERSITY

The report found between 65 and 70 per cent of rivers would be deemed swimmable under proposed Government standards.

The risk of getting sick from a river deemed swimmable under those standards, averaged across time, was between 1 and 3.5 per cent.

While much of the water quality debate had been around swimmability, the report highlighted serious issues around the health of native species.

They faced serious threats, largely due to humans. They included degraded habitat through contaminated water, altered flows, and introduced predators.

"Recently there has been a strong focus on how swimmable our waterways are, but that is just part of the story. The implications for our freshwater species are really critical," Robertson said.

"Many of our species are found nowhere else in the world so it is even more crucial we don't lose any under our watch. We need to consider the resilience of all species in any decisions we make that affect the environment."

The report said 72 per cent of native freshwater fish were threatened by or at risk of extinction, including four whitebait species, lamprey, and longfin eels.

One species, the once-common grayling, is already extinct.

A third of native freshwater invertebrates were in the same category; 10 per cent were in the highest threat category, nationally critical.

"A lot of our native species are endemic, so if we lose them they're gone forever," Robertson said.

The report also looked at the cultural health indicators of rivers and lakes, as determined by local Maori.

The results were mixed: about half of sites measured for cultural health were rated moderate, with similar numbers rated good and poor.

Mahinga kai, however, was deemed poor or very poor at 71 per cent of sites.

WATER FLOWS

The report looked at water quantity and found data gaps and uncertainty about how water usage affected waterway health.

Most of the water extracted was used for irrigation, the majority of which (64 per cent) is used in Canterbury.

It was not clear how much of that water was actually used. Using Canterbury as a case study, the report found some consented irrigators used less than their allowance, but some used more.

A "large proportion" of consents had no records at all, meaning there was no data to assess.

That data was from 2013 and many more users now have water meters.

Based on consented water takes (not actual water taken), the report said irrigation had "the highest potential to cause widespread reductions in downstream river flows, compared with other water uses".

It was particularly true in Canterbury and Hawke's Bay, where many takes were from groundwater.

"Our reliance on irrigation, especially in drier regions, to support our economy, has the greatest potential of all uses to cause altered flows downstream," the report said.

Climate change would exacerbate water quantity problems, with lower rainfall expected in already dry parts of the country.

DATA GAPS AND THE FUTURE

The data for measuring water quality was imperfect, with several noticeable gaps.

Among them were data on long term flow levels, how much water was being used, and information on the relationship between land use and water quality.

"The more studies there are, the better we understand the impact people have on fresh water," MacPherson said.

"However, we can't wait for perfect data to act. This report identifies some key issues we can focus on for actions."

The report showed phosphorous concentrations were decreasing in some waterways, indicating improved erosion and fertiliser management, and over time there had been better addressing of point-source pollution.

"We must explore more ways to effectively improve our most vulnerable waterways," Robertson said.

"Past experience shows where we focus our energy, we can make a difference."

The report's conclusions were welcomed by scientists and environment and industry groups, however the gaps in the data proved a matter of contention.

Forest & Bird said the report largely drew from data more than three years old.

"Unfortunately the report doesn't show us up to date trends, which we'd hoped for and which we think the country needs," said freshwater advocate Annabeth Cohen.

The group welcomed the data around freshwater species, and urged the Government to act.

"Large numbers of our freshwater plants and animals are at risk of extinction - their habitat is being developed or degraded at an alarming rate."

Irrigation NZ said the report was based on "limited data" which made it difficult to track progress.

"We know that where farmers and growers are focussing their efforts, they are making a difference. This report does reflect this to a degree, but it is very constrained due to incomplete or inconsistent data," chief executive Andrew Curtis said.

Data around irrigation, particularly how much water was being used, was still incomplete.

"Despite the fact that irrigators have been collecting water measurement data for a number of years, none of it was captured in this report because there is currently no standard measurement, reporting tools or consensus amongst regional councils that allow us to report actual water use data over time."

There were promising initiatives underway to find solutions to the problem, which were not highlighted in the report, said Our Land and Water science challenge director Ken Taylor.

The overall conclusion, however, was welcome.

"We've had a beneficial shift in thinking around water quality which means that no-one is now denying that there's a problem.



"We no longer have to demonstrate there's a problem, there's plenty of information to show that there is, now we need to focus on finding the solutions to the problem."

Dr Scott Larned, freshwater research manager at NIWA, said there were several "big issues" beyond swimmability, such as wetland loss, nutrient enrichment in waterways and invasive species.

The trend of greatest concern was increasing nitrogen levels, due to the legacy effect - it can take many years for nitrogen to reach groundwater, meaning the impact of current practices may not yet be clear.

"It's a concern because it's very difficult to reduce nitrate levels in groundwater, and because the current trend may continue far into the future due to the legacy effect," he said.