Factsheet: Understanding estuaries

Getting to know estuaries

Estuaries are unique places where freshwater meets and mixes with saltwater from the sea. They are sheltered, semi-enclosed bodies of water and are often called harbours, bays, lagoons, inlets, fiords, sounds and wetlands.

The estuaries we see in Aotearoa / New Zealand today were formed between 12,000 and 7,000 years ago. At the end of the last ice age melting glaciers caused sea levels to rise, and as the sea rose it flooded valleys carved by rivers and glaciers to form young estuaries. Around 300 estuaries have been described across the country, and they take various forms depending on the type of landscape that existed prior to flooding. The smallest estuaries in the country are only a few hectares, whilst the largest (Kaipara Harbour) is 52,000 hectares!

Estuaries age much like we do, they have a youth, middle age and eventually die. The aging process of estuaries is controlled by the rate at which they become filled with sediment from the land and the sea. This varies between estuaries and is largely dependent on their size, the size of their catchment, the rate of soil erosion in the catchment, as well as the potential for sediment to become trapped in the estuary.

When young, most estuaries have deep basins and are dominated by open subtidal areas. In their middle age, sediments accumulate in the basin and around estuary edges causing waters to shallow and intertidal sandflats to grow. This increase in intertidal space allows saltmarsh vegetation and mangroves to establish. In old age, estuaries are generally characterised by extensive intertidal sand and mudflats covered in mangroves, with narrow tidal channels. Eventually, the upper reaches of the estuary become elevated and are no longer submerged by the tides, allowing freshwater marshes to establish, and the lower reaches are so filled with sediment that the sea only enters at high tide. At this point, the estuary has died. This aging is a natural process, but human activities that result in excess sediment being delivered to estuaries can speed this up.

Biodiversity hotspots

Physical features of estuaries include deep channels, shallow brackish waters, rocky reefs, exposed sand and shell banks, and intertidal sand and mudflats. The delivery of freshwater and nutrients by rivers also enables estuaries to have incredibly high levels of primary productivity. This combination of physical complexity (providing many habitat types) and an abundance of food is the perfect recipe for high biodiversity.

Most primary production occurs along the shoreline and in the shallow waters of estuaries where light is most available; wetland sedges and rushes, mangroves, seagrass, kelp, even microscopic algae on sandflats contribute. These primary producers can in turn support large and complex food webs. Cockles, sea snails, mussels, shrimp, worms, crabs, urchins, lobsters, rays, fish, birds, sharks and much more, can all thrive in estuaries and depend on each other intricately.

Some species are dependent on estuaries for key parts of their life cycle, despite not living in them permanently. The sheltered waters and abundant food make estuaries great nursery environments for young freshwater and open ocean species. For example, eels (tuna) travel down rivers, through estuaries and out to the ocean to spawn (lay their eggs). The young then return to estuaries as juvenile glass eels and spend several months feeding and growing before returning upriver. Many shark species also birth their young in estuaries, allowing them to use the estuary as a refuge until they are large enough to return to the ocean. Other species may visit daily or seasonally to feed, including flounder, mullet, kahawai, snapper, red cod and gurnard.

Wading birds gather in their thousands on the exposed tidal flats of estuaries, probing, sweeping and sifting for food. At least 70 different bird species may be found within estuaries across the country, with oystercatchers, dotterels, wrybills, spoonbills, stilts, herons and terns, as well as ducks and teal, being some of the characters found. Whilst some live in Aotearoa / New Zealand year-round, others like godwits, golden plovers and lesser knots migrate huge distances to feed in our estuaries over spring and summer. They depend on the algae and macrofauna in the sand and mudflats to provide energy for the return journey and to breed. The critical role of intertidal flats for large populations of wading birds has resulted in many of these habitats being recognised as having regional, national, and even international importance.

Benefits of healthy estuaries

Estuaries are in good health when they have a high diversity of habitats, plants and animals and the connections between all components are intact. Under these conditions, estuaries provide a range of ecosystem services that benefit us. Some of these services are highly visible, such as the production of food or materials, whilst others are less so, such as nutrient cycling or climate regulation. The plants and animals living in estuaries influence the processes and functions that control these services, see the Estuary macrofauna factsheet for more detail.

Healthy estuaries are also more resilient to disturbances, meaning their communities and ecosystem services can bounce back from the impacts of a sudden change. This is because individuals are more resilient plus the high diversity and abundance of plants and animals means disturbed areas can be quickly recolonised, or different species can fill the role of those that have been lost. For instance, the feeding of rays can be described as a disturbance to estuary sandflats, as they move across the sandflat feeding on shellfish and leave large empty patches in their wake. When there are healthy populations of shellfish in the wider estuary, they may move short distances to fill the patches or spawn to produce juvenile cockles that can settle in them.

In addition to ecological benefits, healthy estuaries are more enjoyable places to spend time. Whether this be fishing, swimming, bird watching or enjoying water sports, many social and cultural benefits can be gained from an estuary in good health.

Ecosystems under pressure

The access to food, freshwater, and opportunity to travel and trade on the water has made estuaries popular places for human settlement. The unique location of estuaries means they experience pressure from human activities taking place on land and ‘at sea’. Within estuaries, commercial and recreational fishing directly remove fish, shellfish and more from the ecosystem. Anchoring, trawling and dredging damages delicate seafloor habitats. Ports and marinas may pollute estuaries with contaminants from oil spills and boat anti-fouling paints, and the movement of boats and emptying of ballast waters has the potential to introduce pest (non-native) species to new locations.

Estuaries are also vulnerable to land-based activities because they are at the end of freshwater drainage networks (i.e., catchments). Materials generated in the catchment can ultimately be washed by rain and rivers into the estuary, particularly after heavy rainfall. The clearance of native vegetation for farming, forestry and urban development can lead to excessive amounts of sediment and nutrients entering and overwhelming estuaries. Litter and contaminants can be washed in from towns and cities, and the construction of roads and buildings restrict and reduce the naturalness of estuary shorelines.

Climate change is a global phenomenon that also puts our estuaries under pressure. Sea level rise, marine heatwaves and coastal acidification are some of the consequences of climate change that affect estuaries. These pressures can be more severe in estuaries than the open ocean, given many have shallow waters.  These processes interact with local pressures, and each other, to have largely unknown impacts. For instance, what happens to estuary health when the water is warmer, more acidic, and contaminants are being flushed into an estuary? Predicting the effects of such multiple pressures is very difficult.

If not managed well, the overall effect of these activities and processes is a reduced diversity of habitats and animals in estuaries. For example, excessive fine sediments may smother coarse sand, rocky platforms and seagrass to leave only mudflats, resulting in fewer habitats for animals to inhabit. This reduces the number and quality of ecosystem services that can be provided, means there is less food for people to harvest and makes spending time in the estuary less desirable. Knowing the activities that take place in, on and around estuaries helps us to understand what might be affecting their health and what we can do about it.


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