Declining water quality and increased soil compaction caused by farming are the biggest concerns identified by the first state of the environment report in eight years.
Statistics New Zealand and the Ministry for the Environment have released a landmark national environmental report, Environment Aotearoa 2015.
The report found greenhouse gas emissions and the amount of carbon dioxide in our atmosphere had increased, as had sea levels and ocean acidity.
The main areas of concern were the decline in the diversity and conservation status of indigenous species.
Farming came under the spotlight, with a worsening in the quality in rivers as a result of intensely farmed land, and more than 75 percent of soils under dairying being badly affected by compaction.
However, the report also found emissions from transport, and from wood and coal burning, had declined.
Overfishing, seabed trawling and bycatch of protected species had also reduced.
Secretary for the Environment Vicky Robertson said the report showed a "mixed bag", and she was not surprised by some of the problems found.
"There are some things that are great and improving, and I think for a country that has fantastic natural environment, it points out some things that we can do better in," she said.
Air quality had significantly improved since 2006, which the report put down mainly to a shift to cleaner home heating.
Between 2006 and 2013, estimated emissions for five key pollutants from road vehicles fell between 26 and 52 percent, due to improvements in fuel and stricter emission limits on new vehicles.
It was estimated 1000 premature deaths were linked to particulate matter in the country's air in 2012 - 14 percent fewer than in 2006.
Atmosphere and climate
New Zealand was responsible for about 0.1 percent of global emissions between 1990 and 2011.
Global net emissions of greenhouse gases rose 33 percent in that time but New Zealand's increased 42 percent; carbon dioxide concentrations - the greenhouse gas which has the greatest impact in the long term - increased 21 percent in New Zealand since 1972.
New Zealand's temperature increased about 0.9°C in the past 100 years, which the report said was almost certainly due to the increase in greenhouse gases in the atmosphere.
The report found water quality was good in areas with indigenous vegetation and less intensive use of land.
However, rivers in agricultural and urban areas had reduced water clarity and aquatic insect life, and higher levels of nutrients and Escherichia coli (E.coli) bacteria.
Between 1990 and 2012, the estimated amount of nitrogen which leached into soil from agriculture increased 29 percent, mainly due to increases in dairy cattle numbers and nitrogen fertiliser.
Once in the soil, excess nitrogen travels through soil and rock layers, ending up in groundwater, rivers and lakes.
Between 1989 and 2013, total nitrogen levels in rivers increased 12 percent, with 60 percent of monitored sites showing statistically significant increases.
About 49 percent of monitored river sites had enough nitrogen to trigger nuisance periphyton growth, which the report said was the biggest impact from excessive nutrients.
Periphyton is algae growth which impedes river flows, blocks irrigation and water supply intakes, and smothers riverbed habitats. It also affects recreational use of the water.
Agricultural and horticultural land occupies nearly 42 percent of New Zealand, while plantation forestry covers a further 7.5 percent.
Indigenous forest covers about 25 percent of the country mainly in upland and mountainous areas, while wetlands have been reduced to about 10 percent of their original extent.
The report said the extent of agricultural land had not changed substantially since 1996 but its use had become more intensive in a number of regions.
Compaction was a significant issue affecting the land; compaction occurs when soil is compressed, reducing the air pockets between soil particles, making it harder for plants to grow and therefore reducing productivity.
More than half the soils measured under dry stock farming, such as for meat, wool and velvet, and nearly 80 percent of soils under dairy farming, were affected by compaction.
As well, pests such as possums, rats and stoats were a serious threat to New Zealand's indigenous animals, plants, and habitats.
The most serious long-term pressures on the country's marine environment were likely to be caused by climate change, the report said.
Coastal sea levels and long-term sea-surface temperatures throughout New Zealand had risen during the past century, and our oceans were more acidic than when measurements were first taken in 1998, the report said.
Eight of our 30 indigenous marine mammal species were threatened with extinction.
The extinction risk of one of these - the New Zealand sea lion - had increased in recent years, while Māui's dolphin was one of the rarest marine mammals in the world; only an estimated 55 individuals older than one year remained.
Of the 92 indigenous seabird species and subspecies which breed in New Zealand, 35 percent were threatened with extinction and a further 55 percent were at risk of extinction.
The extinction risk had increased for seven seabird species in recent years.
However, between 2009 and 2014, the proportion of fish stocks subject to overfishing decreased from 25 percent to 14 percent.
In 2014, more than 95 percent of fish caught were from stocks which were not overfished.