Water quality: Farming increases nitrogen run-off
The report found that while water quality was very good in areas with indigenous vegetation and less intensive use of land, it was a different story in agricultural and urban areas where there was reduced water clarity and aquatic insect life, and higher levels of nutrients and harmful E.coli bacteria.
The greatest impact of excessive nutrients in rivers was nuisance slime and algae (periphyton) growth, which could impede river flows, block irrigation and water supply intakes, and smother riverbed habitats.
Between 1990 and 2012, the estimated amount of nitrogen that leached into soil from agriculture increased 29 per cent, which was mainly due to increases in dairy cattle numbers and nitrogen fertiliser.
Once in the soil, excess nitrogen travelled through soil and rock layers, ending up in groundwater, rivers, and lakes.
Between 1989 and 2013, total nitrogen levels in rivers increased 12 per cent, with 60 per cent of monitored sites showing statistically significant increases.
About 49 per cent of monitored river sites have enough nitrogen to trigger nuisance periphyton growth, as long as there was enough sunlight, phosphorus, and a lack of flood events for algae to bloom.
Phosphorus also triggered nuisance algae growth, and about 32 per cent of monitored sites had enough phosphorus to trigger this growth.
High levels of nitrogen could also be harmful to fish, although less than 1 per cent of monitored river sites had nitrogen levels high enough to affect the growth of multiple fish species.
Water clarity improved at two-thirds of monitored sites between 1989 and 2013, while E.coli levels were higher in urban and pastoral areas but met acceptable standards for wading and boating at 98 per cent of monitored sites.
Marine environment: Climate change the key threat
The most serious long-term pressures on our vast and incredibly diverse marine environment were likely to be caused by climate change, the report found.
Coastal sea levels and long-term sea-surface temperatures around New Zealand had risen over the last century, and our oceans were now more acidic than when measurements were first taken in 1998.
Eight of our 30 indigenous marine mammal species are threatened with extinction, and the extinction risk of one of these -- the New Zealand sea lion -- has increased in recent years.
The Maui's dolphin was now one of the rarest marine mammals in the world, with an estimated 55 individuals over a year old remaining.
Of the 92 indigenous seabird species and subspecies that breed in New Zealand, 35 per cent were threatened with extinction and a further 55 per cent were at risk of extinction.
The risk of extinction had also increased for seven seabird species in recent years.
Between 2009 and 2014, the proportion of fish stocks subject to overfishing decreased from 25 per cent to 14 per cent.
In 2014, more than 95 per cent of fish caught were from stocks that are not overfished.
Air and atmosphere: More carbon dioxide, less carbon monoxide
The report found burning wood and coal for home heating was the primary source of pollutants that caused most concern, as it contributed 58 per cent to annual emissions of human-made particulate matter in our air.
This was a problem mainly in winter, in places where households use wood or coal to keep their homes warm.
But air quality showed a significant improvement since 2006, driven mainly by the shift to cleaner home heating.
Between 2001 and 2013, estimated emissions for five key pollutants from road vehicles fell between 26 and 52 per cent, due to improvements to fuel, and stricter emission limits on new vehicles.
In 2012, an estimated 1000 premature deaths were associated with particulate matter in our air, 14 per cent fewer than in 2006.
In the wider atmosphere, meanwhile, the biggest driver of change was the increase in global greenhouse gases.
Global net emissions of greenhouse gases rose 33 per cent since 1990, and between 1990 and 2011, New Zealand emitted around 0.1 per cent of global emissions.
New Zealand's emissions of greenhouse gases increased 42 per cent between 1990 and 2013.
Concentrations of carbon dioxide - the greenhouse gas that had the greatest impact over the long term - have increased 21 per cent since 1972.
New Zealand's temperature increased around 0.9C in the past 100 years, which was "almost certainly" due to the increase in greenhouse gases in the atmosphere, the report found.
Our exposure to high ultraviolet light levels were also part of the reason our rates of skin cancer (melanoma) incidence were among the highest in the world.
Land and nature: Erosion and pests among the biggest problems
While the extent of agricultural land has not changed substantially since 1996, its use has become more intensive in many regions.
The most critical issue affecting our land was erosion caused by human activity, particularly in the north and east of the North Island.
This reduced the productivity of the land and affects water quality, because it added sediment and nutrients to waterways.
Another big issue facing our land is compaction, which occurred when soil was compressed, reducing the air pockets between soil particles, and making it harder for plants to grow.
Over half the soils measured under dry stock - animals farmed for dairy, meat, wool, and velvet - and nearly 80 per cent of soils under dairy farming were affected by compaction, which reduced the productivity of land.
Pests also remained a serious threat to our indigenous animals, plants, and habitats.
Possums, rats, and stoats, the most widespread of our pests, were found across at least 94 per cent of the country.
The report noted how our land had undergone extensive change since human occupation 700 to 800 years ago, and particularly since European settlement in the 19th century.
Today, agricultural and horticultural land occupied nearly 42 per cent of New Zealand, while plantation forestry covered a further 7.5 per cent.
Indigenous forest covered about one-quarter of the country, concentrated mainly in upland and mountainous areas, and wetlands had reduced to just 10 per cent of their original extent.
• The independently-produced report was produced in the spirit of the recently-passed Environmental Reporting Act, and is the first of its kind since 2007. The next report - about fresh water - will be released next year.
Nick Smith: Freshwater, climate, biodiversity top challenges
Environment Minister Nick Smith, who had no input or influence in the report, said the report showed the key challenge areas were freshwater, climate change and biodiversity.
New Zealand was making good progress in reducing air pollution that caused urban smog and many premature deaths, and our fisheries were being more sustainably managed with fewer stocks overfished and significant reductions in seabird bycatch, Dr Smith said.
The report on freshwater was however a "mixed bag", he said, and varied significantly around the country.
While water clarity and pollution from ammonia-nitrogen was improving, the trends for total nitrogen and dissolved phosphate were negative.
"While the report finds that 96 per cent of monitored freshwater sites are suitable for wading and boating, it does not report on swimming water quality.
"I am advised this is because the data is inconsistent and not nationally comparable. This is an area on which we will need to improve the data."
The report also showed New Zealand needed to "step up its efforts" on greenhouse emissions and climate change, he said.
"We are making good progress on increasing renewable electricity and are on target to achieve 90 per cent by 2025.
"We need to make more progress on transport emissions and we have a huge challenge around agricultural emissions."
The major threat to our biodiversity remained from introduced pests, and the while the Government had increased areas were pests were controlled, the reality was that too many of our native species were in decline, he said.
The Green Party responded to the report with criticism of what it called a "hands-off" approach by the Government, and stated it should trigger "urgent action" to protect indigenous wildlife, rivers, and seas.
"What we need to see from the Government is a commitment to stop subsidising dairy intensification and to strengthen water standards so that it's safe for people and wildlife to swim in our rivers," the party's environment spokesperson Eugenie Sage said.
"We need a much greater investment in pest control on conservation lands and beyond.
"We also want to see a commitment to establishing effective deep sea marine protected areas and ocean sanctuaries to protect marine habitats, and a National Policy Statement for Freshwater Management that actually ensures the water is fresh."
Parliamentary Commissioner for the Environment Dr Jan Wright welcomed the report, and said she would be publishing a commentary once she'd examined it.
"Environmental reporting is important for diagnosing the health of our environment and helping us to prioritise action."
Dr Wright noted the Environmental Reporting Act, passed last month, required the production of environmental reports at regular intervals - and at arm's length from the Government.
Dr Marie Brown: Power of private interests must be rebalanced
Environmental Defence Society policy analyst Dr Marie Brown said this report had been needed for many years - but the "real acid test" of national environmental reporting was how effectively it would be taken up into the policy space.
"From an initial review, it would seem that there are many useful nuggets of information that should prompt policy innovation," she said.
"Ample justification in the figures exists for strong and effective environmental bottom lines for freshwater management, robustly addressing our carbon emissions, investing in the protection of indigenous biodiversity through protection, management and restoration.
"All of these rely on multi-stakeholder commitment, and Environment Aotearoa 2015 would be most effective if it strengthens resolve to kick these aims along and ensure they deliver for our environment."
Earlier this year, Dr Brown and co-authors released the book Vanishing Nature: facing New Zealand's biodiversity crisis.
"In it we noted that the power of private interests have effectively constrained environmental protection attempts - the results of this lost contest are clearly demonstrated in land, freshwater and marine data presented."
In-progress policy moves, such as the development of a strategic framework for marine protected areas, implementation of farming within limits and bolstering of environmental monitoring by regional councils and other agencies, were all vital to turning this tide, she said.
"Further work is needed in boosting the funding of the Department of Conservation and our environmental sciences in general, introducing clear and effective legislation to protect threatened species and ecosystems and in curtailing the still significant loss of habitat that is occurring across the landscape, such as the loss of tussock grasslands, lowland forest and wetlands.
"For much of our natural heritage, there's little time to waste and mandatory environmental reporting has the potential to provide a strong platform to prompt necessary action."
