The Prime Minister's chief science adviser, Professor Sir Peter Gluckman, has today released an independent report on the state of New Zealand's under-pressure freshwater systems. Science reporter Jamie Morton looks at five headline findings from it.

1. Our lakes and rivers are under increasing stress

Agricultural intensification, urban expansion, industrial pollution, hydroelectric development, the impacts of drought: all are loading pressure on our lakes and rivers.

Our wetlands have been greatly reduced; many catchments are now significantly affected by dam systems; and over recent decades, flows of foothill catchment or spring-fed rivers and streams have declined - particularly in lowland areas on the eastern sides of both islands.

"Many freshwater systems continue to be under increasing stress," the report stated.

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"Overall, there is a mix of both positive and negative trends, but there is evidence that restoration activities are having some positive effects."

There were also improving trends in urban and pastoral areas around phosphate and ammonia - yet the reverse was true for nitrate and total nitrogen.

"There are also improvements in visual clarity and median E. coli concentrations in some areas, but others show progressive deterioration."

General patterns around river and lake water quality are strongly linked to the environment they lie in: those with predominantly urban and pastoral land-cover are typically associated with the poorest water quality, and those with natural land cover, like native forest or tussock, typically have the best water quality.

For both rivers and lakes, concentrations of nutrients like nitrogen and phosphate, along with levels of microbial contamination, increased with rising proportions of high-intensity agricultural and urban land cover in their catchments.

Data from between 2009 and 2013 indicated that median water clarity in "natural" land area was almost twice that in pastoral, urban and exotic forest areas, while the minimum acceptable state for E. coli was exceeded at times at all urban sites and the majority of pastoral sites.

Analyses of 10-year trends from 2004-2013 indicate improvements for many rivers in median concentrations of total phosphorus, dissolved reactive phosphorus, and ammonium nitrogen, and in visual clarity and E. coli, but others still show progressive deterioration.

There were more sites showing degrading trends in MCI scores (indicating declining ecological health) than the number showing improvement, and many sites showed degrading trends in nitrate-nitrogen.

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2. We're to blame for what's happened

The sorry state of many of our lakes and rivers can ultimately be put down to one thing: us.

Humans have dramatically changed the freshwater environment through deforestation, draining wetlands and establishing settlements around freshwater rivers and lakes.

We have brought about big shifts in river flows by clearing large tracts of scrub and forest, and by increasing floods through run-off from the land.

We've also changed the picture through hydropower dams and weirs, and we've introduced a host of alien plants, animals and fish, pushing out native species and transforming important ecological processes.

The rapid intensification of agriculture and the pressures it has brought - including irrigation - is reflected in water quality trends in pastoral areas. Photo / File
The rapid intensification of agriculture and the pressures it has brought - including irrigation - is reflected in water quality trends in pastoral areas. Photo / File

The two big culprits singled out was urban expansion - polluting rivers and streams with stormwater and industrial waste - and the rapid intensification of agriculture like dairy farming, hitting waterways with nitrogen, phosphate, and sediment, faecal contamination from livestock and extra pressure from irrigation.

"There are inherent lag effects of some land-use practices, such that in some areas we are now seeing effects of inputs into waterways that occurred years and even decades ago," the report stated.

Heaped on top of that will be the coming impacts of climate change on everything from flow regimes and water temperature to biotic invasions and groundwater levels.

3. Measuring and monitoring freshwater quality is complicated

Despite an enormous effort, there remains a lack of systematic monitoring of river and lake fish, wetland ecology and water quality, and groundwater macro-fauna - and no overall nationally integrated water quality monitoring programme that gives a complete picture.

There's also a host of different players that try to monitor trends: principally regional councils and Niwa, but also universities, the Department of Conservation, Fish and Game, councils and many others.

The Ministry for the Environment, with Statistics New Zealand, is now tasked under the Environmental Reporting Act 2015 to report regularly on the state of the New Zealand environment, including freshwater systems.

There's also a wide mix of variables that can be used to assess water quality.
These include physical-chemical variables, which take in factors like temperature, pH, dissolved oxygen, salinity, nutrients; biological variables influenced by nutrient inputs, such as periphyton biomass for rivers, phytoplankton biomass for lakes, and the composition of the macroinvertebrate community, called the macroinvertebrate community index, or MCI.

Then there are indicators that can tell us about how safe the water is for us, such as measures for microbial contamination and pathogens like E. coli, Campylobacter, Cryptosporidium, Giardia, and, in lakes, the potential for toxins from cyanobacteria, often called blue-green algae.

4. The new 'swimmability' guidelines try to combine grading and monitoring

The Government recently announced a move requiring councils to identify where the quality of lakes and rivers will be improved so they are suitable for swimming more often, along with an associated target to make 90 per cent of rivers swimmable by 2040.

Also in its "Clean Water Package" was a different grading system, which attracted much controversy and criticisms that the goal-posts had been shifted.

For its surveillance criteria, anything under 540 E. coli per 100ml is the threshold for "swimmability"; anything above means the risk of infection to someone who swims in the water can be more than 5 per cent.

To ensure that risk remains low, the surveillance criteria also specify that if E. coli concentration on a given day exceeds 260 per 100ml, daily sampling is required until the concentration falls below 260 - when risk is under 1ne per cent, or one in 100 exposures.

"Because storm events in particular can lead to a temporarily high count due to faecal runoff and/or wastewater overload, it is logical to have a rating system that considers the possibility of such extreme measures and focuses on the anticipated range of measurements when people are likely to be swimming," the report stated.

The proposed grading criteria are based around the annual median E. coli concentration, as well as how often the above thresholds are exceeded.

Swimmable water would need to have a median E. coli concentration of no more than 130 per 100ml - a level at which the estimated risk was, at most, 0.1 per cent per 1000 exposures.

Many native freshwater species such as the Canterbury Mudfish have become critically threatened due to human-introduced impacts on waterways. Photo / Supplied
Many native freshwater species such as the Canterbury Mudfish have become critically threatened due to human-introduced impacts on waterways. Photo / Supplied

This meant that at least half the time, there would be a very low risk to swimmers, even in waterways that had the lowest swimmable grade of "C/yellow" or "fair".

The grading also took into account the percentage of time the threshold of 540 E. coli/100ml was exceeded at a particular site.

To meet the highest grade - A/blue or "excellent" - this could occur no more than 5 per cent of the time, and the intermediate threshold of 260 E. coli /100ml could not be exceeded more than 20 per cent of the time.

For the lowest swimmable grade, the 540 threshold cannot be exceeded more than 20 per cent of the time, and exceedance of the 260 threshold must be no more than 34 per cent of the time.

Based on the criteria, an "A-grade" river would have an overall infection risk of less than 1 per cent; a B-grade river would have an overall risk of less than 2 per cent; and a C-grade river would have an overall risk of less than 3.5 per cent.

Yet, in practice, the report added, these risks would be much lower, as higher counts would most often occur when the river was unswimmable for other reasons, such as during or after heavy storms.

5. Our drinking water supplies are generally secure

Municipal drinking water supplies in New Zealand meet the required bacteriological, protozoal and chemical standards most of the time, whether sourced from surface water or groundwater aquifers.

Aquifers are underground reservoirs that are formed by layers of porous rock or sand, through which water can flow.

Water enters aquifers from precipitation or by seepage from rivers, lakes, and reservoirs.
Groundwater in aquifers eventually flows naturally to the surface through springs and seeps, or it can be extracted through wells for agricultural, municipal, and industrial use.

Most municipal supplies that are sourced from groundwater come from confined or secure aquifers - those that are covered by an impermeable layer of rock and sediment that prevents leaching of surface contaminants into the water.

Unconfined aquifers lack this impermeable top layer, so there is very little physical filtration or temporal slowing of contaminant movement into water.

This type of aquifer is not considered to be much safer than surface water, and if used to supply drinking water, the water should be treated for contamination in the same way that surface water supplies are.

Although soil layers above contained aquifers provided a barrier to contamination from human and animal activity on the surface, groundwater could still be contaminated by microbial pathogens from poorly constructed wells, septic tanks or offal pits.

Pathogens could be transported through soils but they die off over time and distance.

Contamination was most likely if there was a direct connection between surface water and groundwater, such as shallow wells near streams.