Water Quality

Water quality is highly variable throughout New Zealand. Although many alpine rivers and lakes have very high water quality, pollution problems in lowland waterways are, in many cases, serious. Our urban rivers are generally the most polluted of New Zealand’s waterways. Nitrate-nitrogen concentrations are worsening at more monitored sites than improving and E.Coli concentrations is affecting our ability to swim in rivers. 5034

Lake Rotorua (Credit: Raewyn Peart)

Water pollution can be divided into two types – point source discharges and non-point source discharges. Pollution from point sources refers to contaminants that enter the catchment from one isolated source such as a sewage treatment plant or a dairy milking shed. Non-point source pollution refers to contaminants that enter the catchment from multiple diffuse sources, such as runoff from pasture or urban areas.

The key freshwater pollutants are described below.


Nitrogen and phosphorus are essential for plant growth however in high concentrations they cause adverse effects on the environment.

Too much nitrogen is highly toxic to fish and some other aquatic organisms and can affect humans and animals that drink the water. These ‘toxicity effects’ occur at relatively high nitrogen concentrations. However, negative environmental effects also occur at lower nitrogen levels due to excessive growth of unwanted plants which degrades swimming and fishing spots and has adverse effects on the aquatic ecosystem.

An excess of nutrients in water can cause rapid growth of plants and algae. In a healthy ecosystem, the natural nutrient levels regulate the amount of plant growth that can occur. When excess nutrients enter the water, this can upset the balance. This may cause exotic weeds to take over, or it may lead to eutrophication. This process occurs when plants and algae grow rapidly, taking over the water body. When they die, bacteria decompose the plant material, using up the available oxygen in the water during the process. This causes the deaths of fish, invertebrates and plant life which are reliant on water-borne oxygen. In the most severe cases, a waterway may become anoxic – seriously lacking in oxygen. This has happened seasonally to parts of some lakes in the Rotorua area. 2006

Another effect of eutrophication can be blooms of specific species of algae which produce toxins. This can be fatal to aquatic creatures and render water unfit for consumption or contact recreation. Avian botulism is similar, derived from bacteria that need anoxic conditions. It is a sporadic killer of birds in lakes during New Zealand summers.


Although eutrophication can occur in all types of water bodies, lakes are particularly vulnerable. This is because, unlike rivers where water is constantly replaced, lake water is held in a basin for many years and is only slowly renewed. This allows nutrient pollution to remain in one area for long periods of time.

Lakes at high altitude and in unmodified catchments generally have high water quality. But areas where the catchment is predominantly in pasture are associated with the worst lake water quality. The water quality of many lakes is thought to have deteriorated over the past 20 years, particularly in shallow, lowland, North Island lakes. For example, the eight lakes monitored by Environment Waikato are all highly to extremely nutrient enriched. However, the quality of some lakes has improved where catchment restoration work has been undertaken.

Lakes with some of the lowest water quality include Lakes Hakanoa and Mangakawhere in the Waikato, and Ellesmere and Forsyth in Canterbury. These tend to be small, shallow lakes, which due to their smaller volume, respond more rapidly to changes in the catchment.


Many rivers are also affected by excess nutrients, particularly in lowland areas. In the report Our freshwater 2017, water quality was found to be worse in low-elevation areas on the east coasts of the North and South islands, inland Waikato, Wairarapa Valley, Rangitikei Manawatu coastal plain, Taranaki ring plain, and the Auckland region. Urban rivers are generally the most polluted waterways. Water quality was better in the major mountain ranges, large areas of the Department of Conservation estate, and in smaller areas dominated by native forests in Northland and the Coromandel Peninsula. 5035 The same report states that urban rivers are generally the most polluted of New Zealand's waterways. 5036


Groundwater is also susceptible to pollution by nutrients. 71 percent of groundwater sites that were sampled from 2012-2014 did not meet the drinking water standard and trends in nitrate-nitrogen are worsening.  5037  Once groundwater is contaminated it is very difficult to clean up. Contamination may occur over a long period of time, and therefore may not be noticed until it is too late. In addition, nitrates that leach into groundwater may eventually find their way into surface water downstream. This can have important implications for freshwater management, as pollution may not appear in the surface water until a long time after the activity that originally caused the pollution has occurred.

Consequently, a rigorous groundwater monitoring programme is important. There are almost 1,100 sites for monitoring groundwater quality in New Zealand focused on aquifers which are an important source of supply or which are considered to be at particular risk of pollution. However, not all catchments are covered. Testing groundwater for nutrient pollution can be a good indicator of the general health of the groundwater, suggesting whether other pollutants such as faecal pathogens and pesticides are likely to be present.


Animal and human faecal matter contains large numbers of bacteria which grow in the gut. Although many are harmless, some of these can cause serious health problems in humans, if they reach water used for consumption or recreation. This can occur as a result of poor farming practices or inefficient waste management systems. These include campylobacter, typhoid, giardia and cryptosporidium. The most common, and easily measured, bacteria found in faecal matter are faecal coliforms, of which E. coli is one species. The commonly used Colilert test measures thermo-tolerant coliforms which primarily originate in the intestines of warm-blooded animals. The results are often presented as E. coli counts. Viruses can also be found in human and animal faecal matter. These include the enteric viruses which cause illnesses such as polio, meningitis and hepatitis. Aquatic viruses can cause gastrointestinal and respiratory illnesses.

Over the summer of 2009-2010, 57 per cent of the freshwater swimming spots tested by regional councils were deemed safe to swim, as low levels of bacteria were found in at least 95 per cent of the samples taken there. However, 11 per cent of the swimming spots tested frequently had high levels of E. coli bacteria, meaning they were generally unsuitable for swimming. The data available suggests relatively stable water quality levels over the past six years. There has been deterioration in some sites, such as Coe’s Ford in the lower Selwyn River near Christchurch, which is no longer suitable for swimming.

Faecal bacteria are also a problem in groundwater. Twenty-three per cent of around 700 monitored sites do not comply with the New Zealand drinking water standard. These aquifers are mostly found in Auckland, Otago and Taranaki. Bacteria counts are highest in shallow, unconfined aquifers.


An increase in the rate that sediment is transported off land within a catchment can bring about marked changes in freshwater ecosystems. The rate of sedimentation of water bodies can be affected by natural factors, such as the type of rock found on the river bed and in the surrounding area. However, excess sediment loads are commonly the result of human activity. The type and extent of vegetation cover over the soil has a major impact on sedimentation rates. Sedimentation rates are typically lowest where land is under mature indigenous forest cover and increase significantly when the forest is removed and replaced with pasture. Sedimentation rates often increase again during the transformation of rural catchments into urban areas however, these rates typically reduce when urban areas become established and soil is covered with paved areas, established gardens and lawns.

An excess of sediment can affect water depths, water coverage, the type of sediment found on the floor (for example the size of the particles) and the clarity of the water. When an excess of sediment enters the catchment it can be suspended in the water, reducing light by affecting water clarity and turbidity (the amount of suspended material in the water). Such environmental changes can bring about changes in vegetation, be detrimental to fish habitats, degrade spawning areas and deplete invertebrate populations.

Many fish native to New Zealand are adapted to spend much of their lives nestled in the rocky beds of rivers and other water bodies. Increased sedimentation fills in the gaps between the rocks, reducing their habitat. Many native species are also strongly affected by reductions in water clarity. Organisms living on the river or lake bed can become smothered by the sediment as it settles out.

The visual clarity of New Zealand’s rivers varies widely but has been gradually improving.17 Rivers with very high levels of sediment, where visibility is sometimes as low as 10-40 centimetres, include the lower Manawatu-, the Waitara in Taranaki and the Waipaoa in Gisborne district. On the other hand, rivers with the best visual clarity (such as the upper Motueka, Clutha and Monowai in the South Island high country) have visibility of up to 10 metres.

The Australia and New Zealand Environment Conservation Council guidelines (2000) state that clarity of less than 70 centimetres, averaged for upland and lowland rivers, will not meet the requirements for ecosystem protection. The recommended minimum for human recreation is 1.6 metres, so clearly at times some New Zealand rivers have been below the recommended guideline.

Another impact of the increased sedimentation of rivers is the increased flood risk as river beds rise. For example, the Manawatu- River flooded in 2004 displacing 2,300 people, destroying 4 bridges and seriously damaging 21 others. At the peak of the 2004 flood, the section of the river passing through Palmerston North was shifting 28 tonnes of sediment every second. Analysis of the sediment indicated that about a quarter of it was valuable topsoil, thought to have washed off from steep pastoral land.

Organic Matter

Agricultural runoff, urban wastewater and industrial waste can transfer organic material to water bodies within a catchment. This can include faeces from humans and animals; proteins, vegetables and sugars from food preparation; and cleaning soaps. When organic matter enters a healthy aquatic environment where there is plenty of oxygen dissolved in the water, naturally occurring aerobic (oxygen using) bacteria will eat the organic material, using up oxygen in the water to do so. Consequently their numbers grow beyond what you would normally see in a healthy aquatic ecosystem.

Freshwater bodies undergo a natural process of re-aeration, where oxygen from the atmosphere diffuses into the water, and this process guards against excessive oxygen depletion. But in systems which are overloaded, oxygen depletion can still occur despite this natural replenishment system. Oxygen depletion can have very serious effects on the health of the ecosystem, as fish and plants need oxygen levels to be maintained in order to survive. Some animals need relatively high levels of dissolved oxygen and seasonal depletion can be enough to remove entire populations. If all the oxygen is used up, anaerobic bacteria (non-oxygen-using bacteria) will take over, decomposing the waste material and producing gases such as methane, hydrogen sulphide and carbon dioxide. 2007

The potential harm caused by organic waste can be measured by its potential to remove oxygen from the water. There is a standard measure known as the biochemical oxygen demand (BOD) which is the amount of dissolved oxygen needed by aerobic bacteria to consume the waste (over a 5-day period where the water temperature is 20 degrees centigrade, measured in terms of the number of grams of oxygen consumed per cubic metre). Thus, if waste deposited in the catchment has a BOD loading which is too high, too much oxygen will be removed from the water by the aerobic bacteria thereby jeopardising plant and animal life.

Over the period from 1989 to 2002 total BOD has decreased steadily in rivers across the country. About half of the 77 monitored sites have shown significant decreases in organic waste and none have become more polluted by organic waste.

The Ministry for the Environment suggests that ‘the improved water quality is probably the result of better management of point sources of pollution, such as dairyshed and factory wastewater discharges.’16 Investment in upgrading treatment facilities has therefore had a tangible impact on the health of New Zealand’s freshwater bodies.

Mataura River

The Mataura River in Southland is an example of one river that has improved as a result of a reduction in point source discharges. In 1975 15.5 tonnes of organic waste from a meatworks were discharged into the river every day. Improvements to the factory’s effluent treatment system meant that by 2000 the factory was discharging just three tonnes per day. Accordingly, the river has shown improvements in health, such as less surface scum and foam. Unfortunately, the river still has elevated nutrient and bacteria levels as a result of non-point discharges.

Other pollutants

A wide variety of other pollutants can find their way into freshwater ecosystems, produced by industrial processes, mining and other human activities. Arsenic is used in a variety of industries such as timber treatment, herbicides, insecticides, mining, smelting, and pulp and paper production. Cyanide is used in some mining processes, which may also discharge a cocktail of other heavy metals. Mine drainage can lead to pollutants being discharged where mines have exposed mineralised deposits or mine waste has been left in contact with water. Such drainage can continue for many years from sites of historic mines. Run-off from roads carries pollutants such zinc, copper, lead and hydrocarbons. Pesticides, including herbicides, fungicides and insecticides can pollute groundwater, and render it potentially harmful to humans and stock. Pharmaceuticals, detergents and other household chemicals can enter freshwater bodies through effluent from wastewater treatment systems.

Saltwater intrusion

Saltwater intrusion is another issue that can be a problem for freshwater resources. It is not common in New Zealand but it is a serious resource management issue in some areas. Saltwater intrusion into low lying coastal aquifers can occur naturally, but it can also be caused by the extraction of too much water from the aquifer.

  1. Such as Lake Okaro, where the bottom waters have been anoxic for over 40 years; http://sci.waikato.ac.nz/farm/content/ecology.html

  2. Ferguson G et al, 2003, Sustainable wastewater management: A handbook for smaller communities

  3. Raewyn Peart, Kate Mulcahy and Natasha Garvan. (2010). Managing Freshwater: An EDS Guide. Environmental Defence Society Incorporated.

  4. Page 25, Ministry for the Environment (2017) Our Freshwater 2017

  5. Page 34, Ministry for the Environment (2017) Our Freshwater 2017

  6. http://www.mfe.govt.nz/publications/environmental-reporting/our-fresh-water-2017

  7. page 55, Ministry for the Environment (2017) Our fresh water 2017

Last updated at 1:59PM on April 3, 2018