An estuary is a partially enclosed body of water, that is either permanently or periodically open to the sea, and that is affected by both runoff from the land and inflow from the sea.

^{e81cf5de-b3e8-4e1c-8159-877b50a91926}  Estuaries are located in the brackish water at river mouths and are one of the most ecologically productive marine habitats. New Zealand has around 300 estuarine systems interspersed along the coastline. They cover over 100,000 hectares, and provide a home for a wide range of species, including mangroves, seagrasses, saltmarsh plants, invertebrates, algae and phytoplankton.

There are many different habitat types within an estuary, such as unvegetated sand and mudflats,  as well as vegetated habitats like mangrove and seagrass. They provide spawning and nursery areas for fish and shellfish species. In addition, estuaries are a critical habitat and food source for migratory wading birds, some which travel to New Zealand from as far afield as Alaska each year.

Rocky reefs are common in nearshore areas around New Zealand’s coast. Intertidal reefs are rocky areas of the coastline which extend between spring low water and the spring high tide mark. They include a variety of habitats, differentiated by exposure and aspect, and host a wide range of organisms including algae, crustaceans, molluscs (shell fish) and polychaete worms (small worms).

The Hauraki Gulf, the northeast coast of Northland, the east coast of the North Island (near Gisborne), the southwest tip of the South Island and the west coast of the Chatham Islands are all important areas for intertidal rocky reefs. Shallow subtidal rocky reefs, to a maximum depth of 50 metres, are found around many parts of the New Zealand coastline. Fiordland, East Cape and the Chatham Islands stand out as being particularly important areas for subtidal rocky reef habitat.

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Many reefs are covered in rich algal forests, which can contain several large kelp species and smaller brown, red and green seaweeds. These provide important habitats for a wide range of sea creatures, including over 2,000 species of invertebrates, which are permanently attached to the rocks. Many of these species are only found in New Zealand.

The presence of lush seaweed beds on rocky reefs is generally associated with high biodiversity, because the beds provide food and refuge for other small organisms. These creatures, which include crustaceans, molluscs and polychaetes, primarily live amongst kelp. They provide an important trophic (the feeding position of an organism in the food chain) link between the seaweed, as a primary producer, and predatory fishes, nearly all of which feed on the small rocky reef animals as juveniles.

Supporting a wide variety of organisms, soft sediment habitats cover 70 per cent of the world’s seafloor, and are found throughout New Zealand harbours, estuaries and open coastal environments. They play a key role in marine ecosystem functioning.

Bottom-dwelling animals burrow within the sediment column (up to two metres below the sediment surface in the case of some crabs and shrimps). Because sediment is an accumulation of particles that have settled to the seabed, it is generally rich in organic matter. Soft sediments are inherently complex: bacteria, microalgae and invertebrates all influence oxygen and nutrient concentrations simultaneously, via direct and indirect pathways.

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The sediment–seawater interface is permeable, so water fills the small gaps between particles and carries oxygen into the sediment. The concentration of oxygen in pore water decreases rapidly with depth in the sediment, so animals living beneath the surface must maintain access to an oxygen-rich supply through maintaining open pores. Also, concentrations of nutrients (released by the breakdown of organic matter by bacteria) are generally much greater in pore water than they are in overlying seawater. The nutrients in pore water act as a fertiliser for algal growth, and the algae can only flourish with a combination of both sunlight and essential nutrients.

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A biogenic reef is composed of the hard parts of living and dead organisms which create structure above the seafloor, and is a highly specialised habitat. They often occur in areas of strong water movement where there is a good food source and little sediment deposition.

^{8a068238-941b-4634-8fbf-79b4bf20f6eb}  Biogenic reefs are formed by colonial tube worms, bivalves such as oysters and mussels, sponges, corals, bryozoans, and coralline algae and can form extensive areas of three-dimensional structures up to two metres tall. Formations such as horse-mussel beds and mangrove habitats are also classed as biogenic reefs. ^{c1d4fb00-9980-4f1b-84d2-2ba3ad0cd69c}  These living reefs are important as they provide a stable home for other marine life in an otherwise featureless seabed.

The distribution of known biogenic reefs around New Zealand is patchy, but they are primarily found in the far south of New Zealand on the Catlins coast and around Stewart Island; in the middle of New Zealand from Kaikoura across to the northwest tip of the South Island, in Cook Strait, and along the Kapiti and Wairarapa coasts, East Cape and the east coast of Northland. Stewart and Chatham islands support the greatest proportions of biogenic reef habitat in New Zealand.

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One of the most biodiverse biogenic reef habitats in New Zealand is rare, and occurs where gravel lying on the seabed is intermixed with the hard calcium remains of shellfish and bryozoans. These areas are called ‘calcareous gravels’ and are home to rich thickets of bryozoans and sponges. A very ecologically important area of these gravels occurs around the northern tip of the North Island near Spirits Bay, where more than 330 species of bryozoans and 220 species of sponges have been found. They also occur near the southern coast of the South Island, off the Otago coast, in the Foveaux Strait and in Tasman Bay.

A fiord is a steep-sided valley that has been carved out by glaciers and then flooded by the sea. The freshwater input comes from the surrounding landscapes, via waterfalls and run-off from the mountains and native forests. The copious rainwater leaches through the rich humus of the beech forest and results in a yellow-coloured layer of freshwater overlaying the denser seawater. This reduces the light levels within the fiords and has resulted in normally deep water species living closer to the surface.

Fiordland has 14 fiords of varying depths reaching up to over 400 metres. The unique climate, vegetation and topography in this area has resulted in some specialised underwater habitats. Species living within the fiords are tolerant to the freshwater layer and reduced light levels.

^{c6f6ce20-a173-49c4-9357-ad679e124e32}  Spectacular large tree-like black corals and sea pens, normally only present in deep water, can be found growing there.

Being enormous underwater structures (usually defined as over 1000 metres high), seamounts in the deep waters of New Zealand’s EEZ are of considerable scientific interest, often hosting unusual or unique groups of organisms and a biodiversity disproportionate to their size and area.

^{853ca36c-2968-4a49-a094-6b962153b3fe}  These environments are not only widely recognised as areas of high productivity, but are also regarded as a fragile habitat because of their poor ability to recover if damaged.

Seamounts can support a very diverse range of life. They provide a hard stable surface for sessile plankton feeders to attach to, and act as oases within large plains of seabed covered in low-lying soft mud. Animals attached to the seamounts receive their primary energy supply from nutrient-rich water currents, which well-up around the flanks of the large structures, as they intercept the ocean currents. In addition, tiny invertebrate prey (zooplankton) which are transported along in the currents become trapped on the seamounts. The seamount communities are also fed by detritus and faecal pellets drifting down from organisms which live closer to the surface. The high productivity of these areas attracts large congregations of fish, which, in turn, attract other species to the surrounding waters, such as sperm whales and sea birds.

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Seamount ecosystems are complex and varied. Many harbour their own unique endemic species. Since the mid-1990s, NIWA scientists have studied a variety of seamount habitats in New Zealand, including those of the Chatham Rise and the southern Kermadec volcanic arc. They found species/taxonomic diversity to be high. A 2004 study of Northland Plateau seamounts recorded three hundred and ninety six species of macro-invertebrate on two seamounts. At least 17 per cent of the species (Bryozoa alone) recovered by the survey are currently undescribed for the New Zealand region, including six genera entirely new to science.

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Hydrothermal vents are commonly found near volcanically active places, such as areas where tectonic plates are moving apart.  As hydrothermal fluids pour out of the vent and react with cold, oxygenated seawater, a number of rapid chemical reactions take place. These ultimately form metal-rich chimneys which provide an important environmental niche for deepsea marine life.

Hydrothermal vents support complex ecosystems of unusual organisms that have developed unique biochemical adaptations to high temperatures and the highly toxic (to land-based creatures) environment. The fluids emanating from the vents contain chemicals that feed microbes at the base of a unique food web that survives without any interaction with the sun.

^{1f91817f-cec8-44c4-bb16-b632a9918d3e}  These microbes use chemicals such as hydrogen sulphide to provide the energy source that drives their metabolic processes. They ultimately support a wide range of other organisms such as tubeworms, shrimp and mussels. ^{3957c7e3-8f23-4cf9-b5c6-1acf8d4f28de}

Scientists have recently discovered new forms of life deep under the sea within these vents. Despite the often very high temperatures, large numbers of micro-organisms grow around the vents, typically as bacterial mats. Many animals are unique to particular vent sites and are not seen even a few hundred metres away.

^{0859e6b6-d912-47bc-98b9-4840355960ee}  Deepwater hydrothermal vents in the Kermadec Islands support extensive beds of giant vent mussels, which are unique to the area, and which in turn provide habitat for deepwater crabs and an endemic eel-like fish.