The process of separating commercial minerals from the ground results in waste product known as mine tailings. Tailings are fine grained solids which consist of a slurry of ground up rock, water and chemical residues. Because of the volumes of waste involved, mining companies tend to want to dispose of the waste close to the site. The tailings may be deposited into open pits, underground, or constrained behind a dam. Tailings dams are located at four current or former mining sites in New Zealand. Two of these are in the Hauraki district, one in the Matamata Piako district and one in the Waitaki district.

Mining activities can also result in the diversion of streams around the pit as occurs at the Rotowaro open cast coal mine near Huntly. Runoff from mining sites and from tailings dams that are left behind can cause damage if not properly controlled, even after the mine has ceased operation. Where unmanaged the runoff is often highly acidic and contains a cocktail of dissolved heavy metals and other substances. This is known as ‘acid mine drainage’. The runoff leaches into streams and has serious effects on freshwater ecosystems, by increasing the acidity of the water and polluting them with toxic substances

Rivers are normally neutral or slightly acidic, but never naturally as acidic as can be caused by acid mine drainage. If acid drainage reduces the pH of the waterbody to less than 4, all fish and most invertebrates are likely to die. Acid runoff can be generated rapidly in rain events and then dry up after the storm.

Acid mine drainage has been a significant problem in historic coal mining areas on the West Coast of the South Island. It is estimated that around 125 kilometres of streams are adversely affected by acid mine drainage in this area. It is well recognised internationally that acid rock drainage processes from inadequate mine waste management can take prolonged periods to develop and have been documented to persist for in excess of 300 years.

Water discharged from coal mines, when unmanaged,  can also contain high levels of dissolved iron, aluminium and other metals which are potentially toxic to freshwater life. Gold mining can cause toxic substances and heavy metals such as arsenic, cadmium, lead, antimony and zinc to contaminate waterways. Even where the water runoff from the site is not very acidic, the presence of dissolved heavy metals will affect fish and insects.

In the past, mining had a significant impact on water quality. Mines could discharge silt and sediment into the catchment, as well as processing chemicals and heavy metals from the rock. Nowadays, mines have relatively effective treatment systems, which minimise the amount of silt and sediment being transferred into the catchment (for example by holding waste water in pools to allow sediment to settle before releasing it into the river).

Gold mining gives rise to particular risks because, when the mineral ore containing sulphides is exposed to air and water, the metals can react chemically, dissolving and entering groundwater and streams. This can cause the catchment to become more acidic. The industry has methods to minimise the risk of this by transporting the rock to a treatment plant in a slurry, separating off the water, and then treating it to remove the heavy metals before discharge.  

Mining often changes groundwater flows, and water flowing through exposed ore remnants or mine waste can acquire high levels of heavy metals, with such contaminated flows often continuing long after the mining has ended.

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Gravel is mined from river beds in many parts of the country. Rivers close to urban centres are favoured, to keep transport costs to a minimum. Most gravel extraction takes place from alluvial rivers draining catchments where greywacke forms the dominant rock type, which is supplied to the river bed by erosion upstream.

Over-extraction of river gravel can lower the level of the river bed, change the profile of the channel and alter the composition of the riverbed sediment. Lowering of the riverbed can affect bridge stability as occurred in the Oreti River in Southland and the Wairoa River near Nelson. Extraction can also have downstream effects as it changes the amount of gravel supplied to the coast, potentially causing river mouth lagoons to become unstable and coastal erosion to be accelerated.

Gravel extraction from rivers can damage invertebrate communities by altering the composition of the riverbed, both at the extraction site and further downstream, decreasing habitat diversity. When gravel is removed the composition of the riverbed changes, as finer silt and sediment and exposed bedrock is left when the gravel is removed. This creates a far more uniform surface, and makes the river flow in a more consistent way than it did when gravel of varying sizes lined parts of the river bed. This means that there are no longer eddies and depositional zones in the river which are conducive to the development of diverse invertebrate colonies. A study of the Kakanui River near Oamaru found a decline in the total abundance of invertebrates, in the number of different species present and in the percentage of sensitive species such as mayflies, stoneflies and caddisflies, downstream of the gravel extraction site.

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