Estuaries are an essential part of our coastal environment. They are important to recreation, such as boating and swimming, commercial and recreational fishing and as a refuge and nursery for wildlife. Estuaries provide shelter and food for a variety of birds, fish and other animals. They are also places where the biggest populations of people tend to congregate. Cities and towns were commonly formed around harbours because the main form of transport was once shipping.

Estuarie and birds.

What is an estuary?

Map.An estuary is a sheltered, enclosed or semi-enclosed body of water where fresh and salt water mix. Estuaries generally have large sand and mud flats which are exposed at low tide and covered at high tide. There can be several estuaries within a harbour.

There are 301 estuarine systems that have been identified in New Zealand, ranging in size from a few hectares to more than 1500 hectares. Of these 301 systems, 164 are bar-built estuaries, 56 are drowned river valleys, 65 are lagoons and 16 are fiords.

The story of most of New Zealand's estuaries begins about 10,000 years ago in the Holocene period - which was the time of the last Ice Age. At the end of the Ice Age, the sea levels of the world rose dramatically as the ice melted. Many of Northland's estuaries have been formed in this way and are classified as drowned river valleys.



Estuaries are among the most productive places of all, when compared with other biological zones. Scientists say they are four times more productive in plant matter than fertile farmland, and 20 times more productive than the open sea. Estuaries grow a wide variety of plants which provide food for crustaceans, fish, birds and animals. In estuaries, most of the primary production occurs in the marshes and mudflats where wetland plants such as sedges and rushes, mangroves, bottom-dwelling algae, sea lettuce and eelgrass grow in abundance.

Herbivores only manage to eat a small part of the plants produced in the estuary. The rest - over 90 percent - dies down to become food for a host of bacteria, fungi, protozoa and other micro-organisms. These, in turn, become food for bigger consumers such as crabs, bivalves, snails and fish. This is an example of the complicated food chains forming a food web in the estuary. Each organism is depending on others for survival, with all of them linked. Estuaries support up to five times as many bird species as an equivalent area of native bush.

A Northland study has shown that about 30 species of marine fish use estuaries at some stage of their life history and these sheltered havens are an important breeding and nursery area for snapper, flatfish, kahawai and whitebait. Many fish enter the estuary to take advantage of the rich food supply found in the eelgrass beds and intertidal sandflats.

Studies overseas have shown that more than 90 percent of marine species can be found in mangrove estuaries during one or more periods in their life cycles. Of fish caught commercially, 80 percent were linked to food chains dependent ultimately on mangroves.

Estuaries productivity.

Where fresh and salt water mix

The mixing of fresh water and sea water is an important and distinct feature of the estuary. Fresh water, being lighter or less dense than salt water, will flow above the heavier sea water. In estuaries where large amounts of freshwater are discharged, a salt wedge is formed.

This is a wedge-shaped, bottom layer of sea water, which is pushed up the estuary along the river bottom with each incoming high tide. The separation between fresh water and salt water can break down on an outgoing low tide when the waters swirl around more. Such conditions of mixing will create zones of brackish, or diluted sea water, a common physical feature of estuaries.

Sediment traps

Estuaries collect sediments from the ocean and from the rivers that feed into them. Sediments can be sand or mud and silt. This swirls around in estuaries with the waters that mix there from the sea and rivers, until it settles to form sand and mud flats. These areas become rich environments for plants and creatures to set up homes. The plants and trees, such as mangroves that take root there, help to stabilise the sediment. An electrochemical reaction when sediment-laden fresh water meets salt water also causes the sediment particles to clump together and settle to the estuary floor.

Salt marshes

When meadows of eel-grass establish on the foreshore of the mudflats, they start a chain of events that leads to the creation of a salt marsh.


Their roots help bind the underlying muds and silts together, while the sheltered water around their leaves and stems encourages more sediment to settle. At the same time, the steady turnover of plant matter adds its rotting remains to the fertility of the soil, cultivating conditions suitable for other plants to grow. When the soil becomes too fertile, the eel grass can no longer grow. Often the first plant to take over from eel-grass is glasswort (Sarcornia quinqueflora) which covers the young salt marsh with creeping mats. Glasswort lives in Northland estuaries and tastes salty, but sheep love to eat it.

Another pioneer plant may be sea rush (Juncus maritimus) often with jointed rush (Juncus articulates) growing further inland. After these the mangrove tree may become established.


As the tides ebb and flow between the stems of these first salt marsh plants, the silt accumulates and the salt marsh begins to teem with a changing community of animals. Instead of burrowing marine worms, there are earthworms, spiders, beetles and many other insects. Over several centuries, the stage is reached where the salt marsh is rarely covered by the tides. Then it is known as a salt meadow. As the salinity lowers and drainage improves, coastal scrub such as raupo, flax, seedling trees such as manuka, cabbage trees and other plants begin to take over.

Meanwhile, further out the eel-grass continues to trap more silt and new salt marshes are created.





The temperature of the water in the estuary is important because it affects the amount of dissolved oxygen that water can hold. Aquatic organisms are dependent on dissolved oxygen for survival.

Available oxygen varies according to temperature, water turbulence (fast-flowing, choppy water has more oxygen) and the amount of plant life - during the hours of light, plants are photosynthesising, so oxygen is produced and available for animals. At night, plants are respiring and using the available oxygen for themselves.

Clean water has many organisms living in it. Polluted water usually has fewer animals and not so many different types. Some will have been killed directly or by lack of oxygen, or may have been forced to move away.

Sediments can be particles of sand, silt or clay. In the natural process of erosion by streams or rivers flowing to the sea, sediments are transported and deposited, and eventually end up on the sea floor. Very light sediments remain floating in salt water.

However, the rate of sediment build-up in estuaries has been accelerated by human activities, such as new housing subdivisions, road works and other major construction sites. Sediment build-up was about 0.5mm per year, a hundred years ago, but now it is about 6mm a year. In another 100 years, that will total 60cm.

What lives in estuaries?

Pied stilt.Pied stilt (Himantopus lucocephalus)
Studies done in Northland have found that at least 30 commercially important species of fish use estuaries at some stage of their life cycles. These include flounder, mullet, rock fish, sole, kahawai, trevally, parore, red cod and gurnard. Freshwater eels, salmon and whitebait migrate through estuaries at least twice in their life cycle. Beds of shellfish, including pipis and cockles, are exploited in many estuaries and oysters are cultivated on marine farms in many northern bays and inlets.

Wading birds such as oystercatchers and banded dotterels dig for worms and shellfish in the tidal zone. The pied oystercatcher eats an average of 368 cockles per day in winter, and 261 per day in summer. Red-billed gulls love to steal the opened cockles left by the oystercatcher.

Crab.Other wading birds come from the other side of the world to spend the summer in New Zealand estuaries, the most common being eastern bar-tailed godwits and lesser knots. Waders that breed in New Zealand include oystercatchers, herons, banded and New Zealand dotterels, pied stilts and wrybills.

Snail.The tunnelling or short-eyed mud crab (Helice crassa), is found in the high tide zone of sheltered muddy shores around New Zealand. They feed on the particles in mud such as decomposing algae, when the tide is out, and are eaten, in turn, by gulls, kingfishers and some coastal fish such as flounder and mullet. They dig themselves a burrow and only move out of the burrow to feed.

Mud snails live in the upper part of the inter-tidal zone, often among mangroves and salt marsh plants where it is only covered by the tide for a short time. It is muddy brown in colour, and about the same size and shape as a garden snail. Mud snails eat twice their own weight in mud every hour, extracting food material from it.

Native freshwater fish, such as eels and whitebait, lay their eggs in estuarine waters and the young fish are swept out to sea before returning to swim up streams where they mature.

There are 13 species of whitebait (inanga) in New Zealand. The adult fish spawn in autumn, following summer migrations downstream to estuaries. The spawning grounds are on banks of tidal rivers, where slightly sticky eggs become attached to vegetation at high tide. At the next high tide the whitebait hatch and float out to sea. In spring they return as whitebait, possibly to the same estuaries, and migrate upstream.

The free passage of native fish between streams and estuaries can be seriously affected if culverts for developments such as causeways and roads are badly designed.

Life history of two common estuary dwellers -
seagrass and mangrove:

Seagrass and mangrove.

A: The flowers and seeds of seagrass are very small and insignificant. Most expansion is by spreading rhizomes.
B: The adult trees of the Mangrove (Avicennia) flowers in summer, but branches usually don't flower every year. The well-developed seed (propagule) remains in its coat, the pericarp, until the seed drops from the tree. Seeds float for only a few hours before the pericarp is shed, after which the seed settles to the bottom and takes root in the mud.

Importance to Māori

Estuaries and tidal areas have high value to Māori people, providing fish and shellfish, birds, flax and other traditional items. Eels were an important food source, and were caught by hand with an eel-pot or bob consisting of a huhu grub attached to string or flax.

Māori names for some plants and animals of coastal wetlands are:

  • Yellow-eyed mullet - aua
  • Groper - hapuku
  • Flax - harakeke
  • Whitebait - inanga
  • Shellfish - kaeo (or) seafood - kaimoana
  • Cabbage tree- kaauka
  • Kingfisher - kotore
  • Heron - kotuku
  • Mussel - kuku
  • Mangrove - manawa
  • Bittern, matuku
  • Reef heron - matuku moana
  • Crab - paapaka
  • Flounder - patiki
  • Pied stilt - poaka
  • Oyster - tio
  • Rock oyster - tio para
  • Mud snail - titiko
  • Cockle - tuangi
  • Eel - tuna
  • Rushes - wiwi.

Impact on estuaries

The easy access of estuaries means that people and industry can have a major impact. The direct effects of humans include the harvesting of organisms such as sea urchins, snails, bivalves, crabs and flounder for eating or use as bait. The flow-on effect of excessive harvesting on the complicated food webs in estuaries is not yet well known.

Many estuaries have been significantly changed by port or road construction, flood prevention measures or reclamation. Ships flushing ballast water have, in some cases, introduced molluscs and other organisms which may threaten the balance of estuary ecosystems.

Influences on estuaries.

This graphic shows the many influences on estuaries:

  • A: felling bush to open up farm land
  • B: land slips, siltation
  • C: coastal and harbourside subdivision
  • D: reclamation by drainage
  • E: cutting down saltmeadow for farm land
  • F: industrial development and effluent problems
  • G: service roading requiring causeways
  • H: bridges, which restrict inner estuary tidal flows
  • I: rubbish dumping
  • J: cattle grazing
  • K: accidental chemical spills

Types of pollution include:

  • leached nutrients from farm fertiliser;
  • pesticides;
  • oils and dispersants;
  • urban runoff;
  • anti-fouling paints from the ship industry;
  • heavy metals and PCBs from old dump sites and roadsides;
  • oil and bilge spills at boat ramps or refuelling depots; and 
  • sewage from leaks or floods in sewers or inadequate sewerage systems in coastal settlements.

Studies have shown that even small amounts of herbicide spray drift can affect mangroves. Windborne spray from farms and orchards can have a significant impact on leaves and roots, and impair the ability of seedlings to regulate their water and salt intake.

Heavy metals, including zinc, copper, lead, iron and chromium can be dangerous pollutants if excessive amounts accumulate and leach into the estuary. Once they enter the food chain, they can become concentrated in the tissues of marine animals and become dangerous for people to eat.


Most water eventually drains to the sea from the land. Whenever there is heavy rainfall, the drainage systems in cities, towns and roadsides direct the water through pipes and into the sea. Any pollution and debris the stormwater picks up along the way ends up in the sea as well. In some places in Northland, it is not safe to swim or collect shellfish in estuaries straight after heavy rainfall because of all the pollutants that have been deposited in the water from the land and roadsides.

The many shellfish that live in estuaries, such as cockles, are filter feeders that sift through water to get their food. If there is pollution in the water, they tend to filter that as well, meaning they can become unsafe for people to eat. Shellfish help improve water clarity by filtering sediment out of the water. However, if there is too much sediment or pollution, the shellfish will die or move out. This makes the sediment problem worse because there are no shellfish left to filter the water.

Foreign invaders

The shipping industry can have a major impact on estuaries and the coast because ports are often located near the mouths of major harbours. There is a danger of spills during the loading and transfer of cargo at the ports as well as when ships flush the ballast water they carry to stabilise their loads.

Unwanted foreign organisms have already been found in northern waters, including the Asian date mussel which has been found at Onerahi beach in some numbers, and the Pacific rock oyster which has taken over the habitat of the northern rock oyster. The date mussel forms into dense mats which smother other marine life. An imported tube worm has been found attached to the bridge supports in the Whangarei Town Basin.

The Ministry of Fisheries has identified six potential marine pests and wants the public to help by keeping an eye out for unwanted species.

The most feared potential pests are:

  • Mediterranean fanworm, forming dense beds which smother other species and foul marine farms and boats;
  • European shore (or green) crab, which attacks a wide range of sea creatures and threatens scallop and mussel industries;
  • Northern Pacific seastar, which threatens marine biodiversity;
  • Chinese mitten crab, which threatens marine communities and freshwater riverbanks. The crab digs holes into riverbanks, causing them to collapse. It also carries a lung fluke worm which can infect people;
  • Asian clams, which smother other shellfish by reaching populations of 25,000 per square metre; and 
  • Green seaweed, which smothers all other plant life in shallow water. This seaweed is used in aquariums. 

The NRC's role

The Northland Regional Council is responsible for the sustainable management of the region's coastal areas. The Council has developed a long-term strategy in consultation with the community called the Regional Coastal Plan. This sets down rules for the use, development and protection of our coast. Currently the plan is under appeal at the Environment Court.

The Regional Coastal Plan for Northland covers the following activities:

  • recreational activities such as boating and water skiing;
  • structures;
  • reclamation and impoundment;
  • discharges to water;
  • taking, damming and diversion of coastal water;
  • dredging and dredging spoil disposal;
  • moorings and marinas;
  • marinas;
  • marine farming;
  • port operation and development;
  • sand, shingle and mineral extraction; and 
  • network utilities and services. 

What can you do?

Our coastal waters and habitats are described as generally high quality by international standards. However, they are under stress near large estuarine towns and cities, and near the mouths of large rivers. Experts estimate about 390 million tonnes of sediment are washed from the mainland into the sea each year, which badly affects estuaries.

Estuaries are also threatened by the invasion of exotic species such as the Asian date mussel and Undaria seaweed, brought to New Zealand in ballast water or encrusted on ship hulls. Many estuaries have also been lost or damaged through land reclamations, land developments and other human activities.

People can help keep the sea clean and safe by considering what effects their activities might have.

Don't pour oil, paint, detergents and other pollutants down drains. Land owners can fence off streams from stock and replant with native vegetation to help stop erosion and keep fertiliser from leaching into the water.

Boaties can help by making sure they don't spill fuel or detergent into the harbour from their bilge water when they are refuelling or cleaning their boats. Respect marine reserves as no-take zones and stick to the rules on the quantity and size of fish that can be taken elsewhere.

Let the Northland Regional Council know if you see anything that might be a risk for the estuary, like illegal dumps, pollution spills, strange new marine organisms or anyone cutting down or pruning mangroves without a permit.

The Northland Regional Council's environmental hotline is 0800 504 639.


Sources: Studying Temperate Marine Environments, Ocean and Shoreline Management, The Estuary Kit, The Mangrove Resource of New Zealand, Ecology of the Upper Waitemata Harbour, Coastal Wetlands. Mangroves in New Zealand, Between the Tides, Forest and Bird (February 2000). New Zealand's draft Biodiversity Strategy