A major report out today makes a sweeping assessment of how our lakes and rivers are faring, and the news isn't good. Science reporter Jamie Morton takes a look at what it reveals.

Another major stocktake has painted a grim picture of New Zealand's freshwater environment, showing that nitrogen levels are rising and three-quarters of monitored native fish species are nearing extinction.

The 100-page report, published today by the Ministry for the Environment and Statistics New Zealand, has been described as "damning" by the country's largest independent environmental organisation, which is calling for a dramatic reduction in cow numbers.

The report, measuring a range of indicators including water quality and quantity, and the welfare of biodiversity, confirmed that urban waterways were the most polluted, but declining trends in pastoral areas were just as concerning.


Levels of the harmful bacteria E.coli were 22 times higher in urban areas and nearly 10 times higher in pastoral rivers, compared with rivers in native forest areas.

Of the 39 native fish species covered by the report, 72 per cent were either threatened with, or at risk of, extinction.

The report also included dismal trends for two key nutrients, nitrogen and phosphorus, that increase the risk of river-choking algal blooms and are often linked to agricultural intensification.

It showed how nitrogen levels were worsening at more than half (55 per cent) of monitored river sites, compared with the 28 per cent of sites that were improving.

Phosphorus levels, meanwhile, were improving at 42 per cent of sites — but getting worse at a quarter.

More than half of water allocated for consumptive use was for irrigation — and 65 per cent of that had been allocated to Canterbury, where pressure on rivers and lakes has been especially pronounced.

Secretary for the Environment Vicky Robertson said land use had clearly affected the state of fresh water in New Zealand.

"This report confirms our urban waterways are the most polluted but we are seeing more declining trends in pastoral areas and it's important we do something about it now and continue to track any progress."

Roberston said a recent strong focus on how swimmable our waterways were was just part of the story.

"The implications for our freshwater species are really critical."

A leading environment group says it's time for a dramatic reduction in the number of cows in New Zealand. Photo / File
A leading environment group says it's time for a dramatic reduction in the number of cows in New Zealand. Photo / File

Along with those threatened fish species, about a third of native freshwater plants and invertebrates were also at risk.

"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."

Other recent reports also demonstrated the significant impact from human activity on our fresh water quality and quantity and on our ecosystems, habitats and species.

The Ministry for the Environment was now assessing whether modelled E.coli data could be used as a suitable indicator to track over time the risks of infection associated with swimming in water bodies.

"Although this is still in development, we recognise this topic is an area of great public interest, so we are providing some initial results of this work," the report's authors said.

The Government's new Clean Water Package, widely criticised by environmental groups, proposed a new approach to measuring "swimmability".

For a river to be swimmable under the new guidelines, the risk of getting sick from infection, averaged across time, was between 1 and 3.5 percent.

Environmental Defence Society chairman Gary Taylor said it was now clear that urgent and decisive action was needed.

"It's time to dramatically reduce the numbers of cows in New Zealand," Taylor said.

"I think the best way to do this is to require all farming to obtain a land-use consent that should set stock numbers at levels appropriate for the type of land in question, and that will prevent excessive pollution.

"This will require a change in resource management practice so that we focus on reducing stocking numbers where we have serious water quality issues."

How polluted are our waterways?

The report investigated rates of nitrogen and phosphorus, as well as the bacteria E.coli, a key indication of faecal contamination.

High concentrations of the nutrients could lead to too much growth of algae in water, which could then decrease oxygen levels, prevent light from penetrating water, and change the composition of freshwater plant and animal species that live there.

High concentrations of nitrogen could be toxic to species and make water unsafe to drink.

In urban environments, contaminants enter water bodies mainly through stormwater and wastewater networks, illegal connections to the networks, and leaky pipes, pumps and connections.

In agricultural areas like dairy land, nutrients and pathogens stemmed from animal waste and urine, and fertilisers.

An adult giant kokopu, the largest of New Zealand's five native whitebait species, is one of those now threatened. Photo / File
An adult giant kokopu, the largest of New Zealand's five native whitebait species, is one of those now threatened. Photo / File

Since the late 1970s, agricultural practices had intensified in many areas of New Zealand, indicated by higher stocking rates and yields, increased use of fertilisers, pesticides and food stocks, and moves to more intensive forms of agriculture, such as dairying.

Agricultural land use was now the world's greatest contributor to diffuse pollution, run-off from the land or filtration through the soil, but since these discharges were hard to measure, the report authors said it was difficult to determine the relationship between specific land use and water quality.

Animal or human faeces in freshwater, meanwhile, increased the risk of illness for swimmers in the area, potentially causing vomiting, abdominal cramping, nausea and diarrhoea.

E.coli detected in rivers or lakes indicated that faecal matter was present.

Yet, of monitored sites, most had "indeterminate trends" for E.coli between 2004 and 2013, meaning the authors had insufficient data to determine a trend at those sites as well.

But the report did show that E.coli concentration was 22 times higher in the urban land-cover class and 9.5 times higher in the pastoral class compared with the native land.

Of 268 monitored river sites in the pastoral land, E.coli trends were "indeterminate" at 65 per cent, improving at 21 per cent, and worsening at 14 per cent of sites for the 2004-13 period.

Sites in urban, exotic forest and native land areas had similar results, but few monitored sites were in these classes.

Meanwhile, the data around nutrient levels showed levels of nitrate-nitrogen in monitored rivers was worsening (55 per cent) at more sites than improving (28 per cent), and dissolved reactive phosphorus was improving (42 per cent) at more sites than worsening (25 per cent) between 1994 and 2013.

Between 2009 and 2013, concentrations of nitrate-nitrogen concentration were 18 times higher in the urban areas, and 10 times higher in the pastoral areas.

Of 175 monitored river sites in the pastoral areas, nitrate-nitrogen trends were worsening at 61 per cent and improving at 22 per cent of sites for the period 1994 to 2013 period.

Other figures in the report showed nitrogen leaching from agricultural soils was estimated to have increased 29 per cent from 1990 to 2012.

But virtually all of New Zealand's total river length — more than 99 per cent — was estimated not to have nitrate-nitrogen concentrations high enough to affect the growth of multiple sensitive freshwater species for the 2009-13 period.

In the same period, dissolved reactive phosphorus concentration was three times higher in the urban areas, and 2.5 times higher in the pastoral areas, compared with the native land.

Of 145 monitored river sites in pastoral areas, trends in dissolved reactive phosphorus were improving at 46 per cent and worsening at 21 per cent of sites between 1994 and 2013.

Similarly, in the urban and native classes more sites were improving than worsening, but few monitored sites were in these classes.

Native species on the brink

The health and mauri (life force) of many of our freshwater ecosystems faced multiple pressures, which could compound one another.

Most of those pressures came from the way we were transforming freshwater environments, through such activities as infrastructure development, draining wetlands, or chanelling rivers.

New Zealand's native longfin eel. Photo / File
New Zealand's native longfin eel. Photo / File

New Zealand's freshwater environment supports approximately 53 known resident native freshwater fish species, 630 known native freshwater invertebrate types, and 537 known native freshwater-dependant plant and algae types.

But the report covered only those species where there was enough data to do so.

Of those 39 native freshwater fish species covered, 72 per cent were either threatened with (12 species), or at risk of (16 species), extinction in 2013.

Native freshwater fish threatened with, or at risk of, extinction included taonga species such as whitebait species inanga, shortjaw kokopu, giant kokopu, and koaro, along with lamprey and the longfin eel.

Declines in conservation status were observed for the Central Otago roundhead galaxias, Canterbury galaxias, black mudfish and lamprey.

Of eight native fish species, two were estimated to have increased in abundance (shortfin eel and upland bully), and four decreased in abundance (longfin eel, koaro, Canterbury galaxias and common bully) between 1977 and 2015.

Of the 435 native freshwater invertebrate types covered, 34 per cent were either threatened with (66 types), or at risk of (82 types), extinction, as at 2013.

Three of the freshwater invertebrate types declined in conservation status, and none improved between assessment periods.

Among those most at risk was the South Island koura — a freshwater crayfish — and all three species of freshwater mussel kakahi/kaeo.

Further, of 537 plant types, 31 per cent were either threatened with (71 types), or at risk of (97 types), extinction in 2013.

Plants that relied on fresh water included vascular plants, mosses, hornworts and liverworts, and green algae that live in and around fresh water.

These plants were threatened by invasive weeds and drainage, and when vegetation was grazed, trampled on or cleared.

Our vanishing wetlands

The authors had no national information on the health of our wetlands, but they did have data that showed their extent.

Wetlands perform many vital functions — they filter nutrients and sediment from water, absorb floodwaters and provide crucial habitats for wildlife — but widespread draining has left only a small portion of them.

In 2008, the extent of wetlands was only 10 per cent of what it was before the arrival of humans and, in some areas, this has led to a loss of biodiversity and natural function.

In Southland, wetlands not on conservation land were reduced by 1235ha, or 10 per cent, between 2007 and 2014-15.

More than half of water allocated for consumptive use was for irrigation - and 65 per cent of that had been allocated to Canterbury. Photo / File
More than half of water allocated for consumptive use was for irrigation - and 65 per cent of that had been allocated to Canterbury. Photo / File

The South Island's West Coast has the greatest extent of wetlands (84,000ha), followed by Southland (47,000ha), and Waikato (28,000ha).

Meanwhile, the cultural health of our freshwater environment was also hurting.

Tangata whenua and hapu groups across the country determined cultural health index scores — supporting kaitiakitanga, or the Maori practice of guardianship — at 41 sites between 2005 and 2016.

Of the 41 sites assessed, 11 had a good or very good overall cultural health index rating.
Twenty-one sites had a moderate rating, and nine had a poor or very poor rating.

Of the 39 sites assessed, 28 had a poor or very poor mahinga kai (food gathering) status, seven sites had a moderate status, and four sites had a good or very good status.

Who's taking the water?

Although New Zealand had an abundance of fresh water, when flows of rivers were reduced, algae and fine sediment could build up and hurt freshwater species.

More than half the water allocated or consented by councils was for irrigation, but the report authors could not say how much of this was actually used.

Regional councils allocated water by giving consents for industrial, energy, agricultural and domestic use.

It was termed either "consumptive use" when the water was not immediately returned to water bodies, or "non-consumptive use" when water was returned to downstream water bodies after use, as in most hydroelectricity schemes.

Between 2013 and 2014, excluding hydro-electricity use, irrigation was the largest consented user of consumptive water by volume (51 per cent) followed by household use (14 per cent) and industry (13 per cent).

Canterbury accounted for 64 per cent of the total consented volume of water for irrigation.

A further nine per cent of the total consented volume was in Marlborough, followed by seven per cent in Otago.

The report authors said the cumulative effect of consented water takes on downstream river flows showed that irrigation had the highest potential to cause "widespread reductions" in downstream river flows, compared with other water uses.

"This is especially noticeable in Canterbury and Hawke's Bay where many consents are from groundwater as well as surface water."

In Canterbury, one of the few regions that had data available on actual water use, records from 2013-14 showed large differences between consented takes (how much water a user is allowed to take) and recorded takes (how much water the user actually took).

This indicated that users who supplied records did not use their full allocation, particularly in early and late summer.

However, in late February, recorded use was near the maximum allowable use.

"A large proportion of the consents had no associated records so, for many users, we do not know how much water they took."

Freshwater issues 'not new' - minister

Environment Minister Nick Smith said the issues identified around nutrients, E. coli, sediment and fresh water ecology were "not new" and were being addressed as part of the Government's fresh water improvement programme.

This included tighter regulation of nutrients, new provisions for protecting water ecology and the development of good management practice for farmers and other water users, as well as $450 million investment in fresh water quality initiatives.

"Our programme is about openly reporting the problems and a practical plan of initiatives which will improve water management."

Smith added the report gave improved information, but not a complete picture of New Zealand's water management.

"Our new national regulations on water metering that took full effect last November will ensure the next report provides far more comprehensive information on water use.

"The other area where more data is required is in respect of sediments.

"Fresh water is one of New Zealand's most valuable resources, and this three-yearly independent stocktake will become a critical reporting document for ensuring positive progress."

But the Green Party hit out at what it called "weak moves" by the Government to address the problem.

"Water quality in rivers in farmed areas is declining fast, but we can take practical steps to stop that decline," the party's water spokesperson Catherine Delahunty said.

"Our rivers need a moratorium on new dairy farms, and an end to subsidies for the large irrigation schemes that promote unsustainable intensive farming in environments that aren't suitable for that kind of farming.

"In cities and towns, we need more attention to improving the quality of urban stormwater.

"This requires greater investment in slowing, filtering and treating stormwater runoff."

Forest and Bird meanwhile responded to the report by calling for a "comprehensive" government package to restore declining waterways.

"We remind the Government that there is a full package of measures to improve freshwater health, reached by consensus in the Land and Water Forum, and our submission on the Clean Water Package will call for these measures and more," said the group's freshwater advocate, Annabeth Cohen.

She also criticised data gaps in the report, adding that the impact of farming was much greater than statistics suggested.

Although the report stated that nitrate-nitrogen concentration in urban areas was 18 times higher than native forested catchments, compared to 10 times higher in rural areas,
Cohen noted that one per cent of New Zealand was urban, compared with 40 per cent pastoral."

Our freshwater is in crisis, and the primary cause is intensifying land use associated with dairy farming," she said.

"We know that there has been more than a 500 percent increase in dairy cows in Southland alone, while their wetlands have decreased by 10 percent."

"The report doesn't draw the obvious conclusions that the recent OECD report did, which makes much clearer links between irrigation, dairy intensification, and worsening water quality."

Ken Taylor, director of the Our Land and Water national science challenge, said he agreed with the overall conclusions of the report about the state of our water quality.

"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."

Taylor said there was already research underway to understand the way that pressures on the land impact on our water quality.

"One of the problems with the report is that it only presents half the story, the bad news half not the good news half.

"In many cases the report points to a lack of data which is unfortunate because there is a lot of available data on these issues which could have been included, this means this picture we're being presented is only a partial one.

"The report is constrained by the Environmental Reporting Act, which limits what can be reported on to the current state and trend of environmental pressures, it doesn't discuss the levels of response which are already going on to counteract these issues.

"We're already seeing promising responses at a community level, in policy and in scientific research working towards offsetting the issues we're dealing with now."