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by  Maggy Wassilieff

At the very edge of the land, the estuary seethes with life. Bacteria, mud worms, crabs, migrating fish, mangroves and oystercatchers – a fascinating ecosystem has evolved in the mud flats of New Zealand’s 300 estuaries. This fragile habitat is vulnerable to time and tide, and to erosion, pollution and other effects of human activity.

Where fresh water meets the sea

What is an estuary?

An estuary is a partly enclosed body of water where fresh water coming down the rivers mixes with salt water from the sea. A range of coastal landforms fit this description, including bays, lagoons, harbours, inlets, sounds, fiords and swamps.

Flush with nutrients and inhabited by resilient organisms, estuaries are among the most productive ecosystems on earth. They provide rich feeding grounds for coastal fish and migratory birds, and spawning areas for fish and shellfish. They are also important in maintaining the quality of coastal waters.

New Zealand’s estuaries

Long favoured as settlement sites by Māori and European alike, New Zealand’s estuaries are intricately bound up with people’s activities on the surrounding land.

There are about 300 estuaries distributed fairly evenly around New Zealand’s coast. Most are small – 200 hectares or less; 30 are over 1,700 hectares, and the largest is Kaipara Harbour at 15,000 hectares. All are recent in origin, having formed within the last 6,500 years, since the last ice age ended. They were created as the rising seas flooded and drowned low-lying coastal river valleys and bays.

Life and death of estuaries

Estuaries are temporary landforms. Rivers carry sediment eroded from the land into them, and tides bring in sand from the sea floor. If more sediment comes in than flushes out, an estuary will age and eventually die: it fills up with so much sediment that it turns into dry land.

Around New Zealand, infilling of estuaries progresses at different rates according to their shape, and the volume of sediment arriving. The fiords of the lower South Island have hardly changed in the last 6,500 years. In contrast, Waitematā Harbour has accumulated metres of sediment and is at an advanced stage of infilling. If sediments continue to accumulate on its vast intertidal mudflats, some areas will rise above the high-tide level and become permanently dry.

Sometimes a dramatic event can lead to the death of an estuary, or a section of it. During the 1931 Hawke’s Bay earthquake part of the Ahuriri Lagoon was raised by over 1 metre, well above the high-tide level.

Accelerated aging

Human activity has increased erosion and changed the flow of rivers into and through estuaries, speeding up the infilling of many. Scientists analysing estuary sediments have discovered that before humans arrived in New Zealand, estuaries filled slowly – less than 1 millimetre of sediment accumulated on the estuary floor each year. In some North Island estuaries, sediments are now accumulating at an annual rate of 20 millimetres.

The estuary ecosystem

Estuary mudflats seem an unlikely setting for some of the most productive habitats in the world, but here at the interface of land and sea life abounds – for the select few. Certain plants, seaweeds and photosynthetic micro-organisms (phytoplankton) absorb nutrients at a fast rate, grow rapidly and produce lots of food.

Estuaries are termed ‘open’ ecosystems because they are vitally linked to the wider environment. Nutrients are carried in from the land via rivers, and from the sea by the tides. Some of these nutrients are then taken out again when animals such as fish and birds leave the estuary. Some are also flushed out to sea on outgoing tides.

Food webs

Living organisms within an estuary co-exist in a network of interdependent feeding relationships, known as a food web. An estuarine food web contains the following elements:

  • Phytoplankton. These microscopic organisms manufacture food by photosynthesis and absorb nutrients such as phosphorus and nitrogen from the water.
  • Detritus (dead organic matter).
  • Microscopic animals known as zooplankton eat some of the phytoplankton. The remainder of the phytoplankton becomes detritus, when it dies.
  • Larger estuary animals such as filter-feeding worms, shellfish and hungry young fish feed on the zooplankton and detritus.

Detritus producers

Mangroves, seagrass and rushes, the dominant plants of the estuary, produce tonnes of rotting leaf material, broken down into detritus. At Pāuatahanui Inlet near Wellington, 38 hectares of seagrass contribute 34 tonnes of plant material to the food web each year, and 30 hectares of sea rushes contribute 189 tonnes.

Natural water filters

Animals that get their food from matter suspended in the water are filter feeders (or suspension feeders). In the case of shellfish such as cockles, their gills and fine hairs (cilia) filter or strain out any food particles as water passes over them. On marine worms, their tentacles act as a filter.

Detritus feeders

Mud snails, crabs and marine worms abound in estuarine muds. They eat quantities of mud, digesting the detritus and discarding the sand and silt. By eating this decaying organic matter, these mud-dwellers become good pickings for the larger animals of the estuary – fish, birds and humans. And by excreting nutrient-rich wastes, mud-dwellers play a critical role in recycling nutrients within an estuary.

Habitat providers

Mangrove and seagrass are also home to rich communities of filter-feeding animals around their roots. At least 30 types of fish also feed in the waters around mangroves. In 2002 at Whangapoua Harbour, juvenile snapper, trevally, garfish, kahawai, gurnard, mullet, flounder and sole were all found around seagrass, but were not so common in water above bare ground. Mangroves and rushes trap sediments entering the estuary and provide an important habitat for native wetland birds such as the bittern, pūkeko, banded rail and spotless crake.

Plants of the estuary

Harsh habitat

The estuary is a hostile environment for most plants because salt dominates. A few grow further back on the shore, where they live in a fluctuating environment of sea water and fresh water. These plants must cope with:

  • varying salinity levels
  • strong currents and storm waves
  • varying exposure to sunlight and wind
  • low oxygen levels in muddy soils.


Seagrass (Zostera capricorni) is the only flowering plant in New Zealand capable of living submerged in sea water. Small and dark green, with ribbon-like leaves, this plant takes root in sandy silts on tidal flats throughout the country. It forms extensive meadows that spread from just above the low-tide level to full submersion in 1 to 2 metres of sea water.

Stems of seagrass creep a few centimetres beneath the mud and become so interwoven with those of adjacent plants that a firm mat develops. This anchors the plants and helps stabilise shifting sediments during the tidal cycle. Over time, sediments build up within and behind seagrass beds, and other flowering plants colonise the higher ground.

Seagrass decline

Seagrass is in decline around New Zealand. In the Avon–Heathcote estuary near Christchurch, seagrass beds started disappearing in 1920, and by 1952 few patches were left. Extensive loss was noted in the Auckland area in the 1930s, and seagrass cover reduced by 25% between 1945 and 1996 in the Tauranga and Ōhiwa harbours, in the Bay of Plenty. There is no general consensus on the reason: it could be fungal disease, or due to extra sediments entering the estuaries and smothering the plants.


New Zealand mangrove or mānawa (Avicennia marina) forms intertidal forests in the estuaries of the far north. At its southern limits (Kāwhia and Ōhiwa Harbour) the species grows in stunted shrublands. In 1996, mangroves covered 22,500 hectares – less than 0.1% of New Zealand’s land area. Like seagrass, mangroves can withstand daily inundation from sea water, but they need to be exposed for at least half the tidal cycle for their roots to absorb oxygen.

The mangrove is a small tree or shrub with a grey twisted trunk, leathery olive leaves and tiny yellow flowers. It produces special vertical breathing roots (pneumatophores) that take in air during low tide. Fruits germinate early and a young plantlet drops from the tree. Equipped with a well-developed root and two fleshy seed leaves, the young plant quickly starts growing if it strikes fresh mud. Those that fall into the tide float away and may establish new colonies.

Salt marsh plants

Salt marsh areas are found at the head of estuaries, landward of the seagrass and mangrove. The dominant plants on salt marsh are sea rush (Juncus kraussii) and jointed rush or oioi (Apodasmia similis), which form dense rushlands up to 1.5 metres tall. Often present is the marsh ribbonwood shrub or makamaka (Plagianthus divaricatus), especially along the banks of tidal streams. Oioi was used by Māori for thatching the outsides of their houses.

Salt meadows

Beyond salt marsh, where the land becomes drier, turf-forming plants are favoured and a salt meadow develops. Saltwort (Sarcocornia quinqueflora), a native succulent, forms distinctive red, grey or green colonies alongside or sometimes intermixed with mats of creeping herbs like remuremu (Selliera radicans) and shore primrose or mākoako (Samolus repens). Saltmarsh vegetation gives way to coastal scrub on dry land, or to freshwater swamp in wetlands beyond the influence of salty water.


In an attempt to reclaim estuary land for farming, cordgrass (Spartina x townsendii) was introduced from England and planted at the Manawatū river mouth in 1913. It formed intertidal meadows which trapped sediment with such efficiency that the estuary bed quickly built up, changing the environment from bare tidal flat to pasture. This plant and two related cordgrasses subsequently spread into many estuaries around New Zealand, changing conditions so markedly that native plants and animals failed to thrive. Cordgrasses are now classified as noxious plants, and attempts are made to remove them.

Small animals of the estuary

To the casual observer, an estuary may appear devoid of animals for much of the day: a few wading birds out on the tidal flats, or perhaps a couple of gulls fighting over a mud snail. But these birds are just one part of an intricate web of living creatures that may number in the millions or even billions.

To appreciate the abundance of estuary life you must consider what is living in the mud. For it is here that detritus (dead organic matter) accumulates, attracting animals in search of food. When the tide retreats, thousands of burrows, tracks and deposits belonging to various types of animals become apparent.

Ozzie mozzie

New Zealand’s native mosquitoes are irritating pests, but they do not transmit diseases to humans. In 1998 an Australian mosquito – the southern marsh mosquito – was found breeding near Napier. Subsequently it has been found in estuaries from Kaipara Harbour in the north to Wairau Lagoon in the South Island. Adult females are aggressive biters and in Australia carry the Ross River virus. Humans infected with the virus may develop flu-like symptoms that last for months. The New Zealand government has allocated $40 million to eradicate this unwanted visitor.

Mud worms

Enormous numbers of worms live in estuarine muds. Known as mud worms or bristleworms, these small segmented creatures are related to earthworms, but are characterised by a pair of short bristly structures on each segment. Some live in permanent burrows, feeding on the organic matter in the mud; others are more mobile and scavenge on the surface or through the mud. Like earthworms, they leave casts of undigested sediment at their burrow entrance or along the trails they make. Mud worms are a significant food source for wading birds and fish.


Three kinds of crab are commonly encountered on tidal mudflats.

Kairau, the tunnelling mud crab (Helice crassa), dominates the upper tidal zone. This extraordinary little crab is found in high numbers on many estuaries, but is easily overlooked. It retreats into a burrow as soon as it detects movement and its grey-olive shell merges with the mudflats. Kairau scoops up mud with its nippers and uses its mouth parts to locate organic matter.

The mid-low tide zone is the realm of another tunnelling crab – the stalk-eyed mud crab (Macrophthalmus hirtipes). It is larger and greener than kairau, and mainly active at night.

The hairy-handed crab or papaka huruhuru (Hemigrapsus crenulatus) is found throughout the intertidal zone. It is not a tunnelling crab and may be found under rocks or just under soft sands and mud. Densities of 255 crabs per square metre been recorded in the Avon–Heathcote estuary.


The cockle or tuangi (Austrovenus stutchburyi) is a shallow-burrowing shellfish, found from subtidal to mid-tide levels. It is not related to the northern hemisphere cockle, and is found only in New Zealand waters. The cockle is one of the most important creatures of the estuary: it provides food and modifies the habitat, playing a critical role in filtering water.

Fresh flesh

In some areas the native cockle or tuangi reaches great numbers. At Pāuatahanui Inlet near Wellington, a density of nearly 550 million cockles to 1 square kilometre was recorded in 1976. This number of shellfish would produce 3,500 tonnes of meat – about the same amount as 7,000 head of cattle.

Cockles are favoured by oystercatchers and sand flounder, and by people. If these shellfish manage to escape the attention of the many predators in the estuary, they can live for up 20 years. They are commercially harvested from Whangārei Harbour, Golden Bay and Otago Harbour – the total catch limit in 2001–2 was set at 2,280 tonnes.

Larger animals of the estuary


In New Zealand at least 30 types of fish use estuaries at significant times in their life. Some, such as sand flounder, yellow-bellied flounder, common sole, kahawai, grey mullet and yellow-eyed mullet, move in and out of estuaries each day. They swim over the tidal flats on the incoming tide searching out shellfish, crabs and worms. Others – snapper, red cod and gurnard – are seasonal visitors. They enter the estuary as immature fish and spend some months feeding in the rich, sheltered waters before heading back out to sea.

Migrating fish

Estuaries are vital to the 17 native fish that migrate between fresh and salt water. They serve as gateways through which the fish must pass to complete their life cycle.

Adult whitebait or īnanga (Galaxias species) come down rivers to lay their eggs among the plants of the upper estuaries in late summer and autumn, and then die. On hatching, the young are swept out to sea, where they spend five or six months. They then enter estuary mouths in spring, and swim upstream to fresh water further inland.

In contrast, adult eels come down the rivers and through the estuaries to spawn at sea somewhere in the tropical Pacific. Their larvae then make their way back to New Zealand’s coastal waters in spring. They transform into a juvenile stage known as glass eels just before they enter estuaries, where they settle and feed for a while before swimming upstream into fresh water.


Tidal flats hold a bounty of food for wading birds, which gather there in large numbers to feed; for individuals, there is little protection on the exposed flats. Mud probers like oystercatchers and godwits push their beaks deep into the sediments in search of shellfish, marine worms and insect larvae. Wrybills feed from the surface of the mud, sweeping their beaks across it in search of insects, small crabs and prawns. Pied stilts search the water and marshy rushlands for aquatic insects, snails and crabs. Others such as herons and Caspian terns are fishers, stalking the estuary waters in search of their swimming prey. Waterfowl such as ducks and teal sieve estuarine waters and mud through their beaks to extract plankton and small animals. The rushes, reeds and mangroves provide sheltered breeding grounds for swamp birds such as the pūkeko, bittern, marsh crake, banded rail and fernbird.

International stopovers

The Ramsar Convention is an intergovernmental treaty which was signed at Ramsar, Iran, in 1971 for the conservation of wetlands used by migratory birds. Through this treaty, estuaries in New Zealand are linked with sites in Australia, Japan, China, Korea, Siberia and Alaska.

Migrating birds

Each year thousands of godwits, plovers and lesser knots travel 11,000 kilometres from their Siberian and Alaskan breeding grounds, arriving in spring at New Zealand’s estuaries. Sheltered estuaries, from Pārengarenga Harbour in the north to Paterson Inlet on Stewart Island in the far south, provide rich feeding grounds for 102,000 eastern bar-tailed godwits and 60,000 lesser knots, as well as smaller numbers of ruddy turnstones, red-necked stints and golden plover. In recognition of their critical role in the life of migratory birds, four large estuaries – Firth of Thames, Manawatū River, Farewell Spit and Waituna Lagoon – are designated Wetlands of International Importance under the Ramsar Convention.

People and estuaries

Māori settlement

Estuaries were favoured food-gathering spots and sites for settlement for the early arrivals from Polynesia. They remain significant areas for fishing and shellfish harvesting.

Estuaries provided safe, sheltered waters with an abundance of fish, shellfish and birds for eating. Middens (ancient refuse heaps) have been found in every sheltered coastal site around New Zealand and are especially common around northern harbours with large shellfish beds. Estuarine rivers gave access to the interior of the country and its wealth of resources – tall-timbered rain forests, abundant bird life, flax swamps and rivers full of eels.

European settlement

When European settlers began arriving in the early 19th century, like Māori they were attracted to estuaries. The large estuaries made excellent natural harbours; cities and towns like Whangārei, Auckland, Tauranga, Napier, Wellington, Lyttelton, Dunedin and Bluff soon developed around them because transport in the developing colony was predominantly by coastal shipping. Small ports sprang up in practically every harbour in Northland and the Coromandel in the 1860s, as settlers stripped the land of its kauri timber and gum and shipped them to large ports at Auckland (Waitematā Harbour) and Onehunga (Manukau Harbour).

Shipping on the Avon–Heathcote

The colonial founders of Christchurch relied on the Avon–Heathcote estuary for transport and trade for the first 20 years of settlement. Until the Lyttelton rail tunnel opened in 1867, small vessels (schooners, yachts, whaleboats) ferried people and goods across the sandbar and up to the Barbadoes Street bridge on the Avon River, or to Wilson Bridge on the Heathcote River. As settlers cleared and drained the land, the rivers clogged up with sediment. By 1900 the Avon was less than 10 centimetres deep in many places.

Food supply or dumping ground?

Because estuaries were viewed by many European settlers as unproductive wastelands, estuarine land was reclaimed for harbours, and filled in for pasture, sewage schemes and rubbish dumps. Māori never accepted this view and actively protested when sewage and stormwaters were discharged into estuaries. A number of claims to the Waitangi Tribunal have focused on the destruction of traditional estuarine food-gathering areas. The spiritual and cultural dimensions of Māori objections were expressed by Ngāti Pikiao claimants in their Kaituna River claim, which stated that ‘to mix waters that had been contaminated by human waste with waters that were used for gathering food was deeply objectionable’. 1

Since the passing of the Resource Management Act in 1991, local authorities have been required to manage estuaries and other coastal areas in a sustainable manner and respect Māori cultural and spiritual values.

Threats to estuaries

Notwithstanding the Resource Management Act 1991, many estuaries remain vulnerable to harmful influences. The major threats are:

  • excess silt flowing in from land clearance
  • pollution from sewage, industrial wastes and agricultural run-off
  • oil spills
  • invasion by introduced species
  • reclamation for marinas
  • extraction of sand and gravel.

These activities decrease the habitat available for estuarine plants and animals, spoil recreational activity in the area, and jeopardise the role estuaries play in maintaining the health of coastal fisheries and waters.

Why value estuaries?

The estuary plays an important and complex role in the life of the coast, acting as:

  • a breeding and feeding ground for fish and birds
  • a buffer for the coast from storms and floods
  • a filter for sediments and pollutants from coastal waters
  • a record of past environments and events
  • a place for recreation (such as water sports, fishing, shellfish gathering, duck shooting, birdwatching)
  • a site for marine farms.

In the past, many New Zealanders failed to appreciate the value of estuaries, as their life in the towns and on farms seemed to be independent of the state of coastal waters. But with an expanding population demanding clean water for recreation and aquaculture, people are learning that healthy estuaries are an asset and deserve careful management.

    • Waitangi Tribunal, Kaituna River claim, Wai 4. Section 3.11. Wellington, 1984. › Back

External links and sources

More suggestions and sources

How to cite this page: Maggy Wassilieff, 'Estuaries', Te Ara - the Encyclopedia of New Zealand, (accessed 17 July 2024)

Story by Maggy Wassilieff, published 12 June 2006