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Estuary Health

Estuaries are partially enclosed water bodies where freshwater meets and mixes with saltwater from the sea. These sheltered features are often called harbours, bays, lagoons, inlets, fiords, sounds, tidal river mouths and wetlands.

Healthy estuaries house a great number of different plants and animals and have high ecological value. They are important mahinga kai / food gathering places and provide opportunities for people to connect with nature and each other.  Estuaries also play a major role in supporting water quality through natural filtration and binding pollutants within sediment. If we can look after estuaries, they can look after us.

In this topic, you can find further information about why estuaries are so valuable and what some of the biggest threats to their health are. You can explore and download monitoring data from estuaries around the country and see national summaries of the available information.

Understanding estuaries

There are over 300 estuaries spread along the coastlines of Aotearoa New Zealand’s mainland and offshore islands. They come in many shapes and sizes and contain a variety of habitats. These can include wetland rushes, sedges and saltmarsh, mangroves, sandflats and mudflats housing seagrass and microscopic algae, and rocky platforms bearing seaweed. Estuaries are often highly productive and support a diverse range of life; birds, shellfish, fish, mammals, and invertebrates, including taonga species like cockles, pipi and pātiki / flounder.

‘Estuary Health’ refers to the ecological condition of an estuary; the state of its plants, animals and physical features and their ability to operate as a system. Health is made up of many factors and is commonly simplified to measures of biological diversity or indirectly estimated through measures of impacts in and around the estuary.

The infographic below shows two extremes of estuary health.

Healthy estuaries Unhealthy estuaries Diversity of habitats Threats to estuaries

About estuaries

Introducing the special places where rivers meet the sea


About estuaries

  • Aotearoa New Zealand’s estuaries were formed between 12,000 and 7,000 years ago when melting glaciers caused sea levels to rise, flooding river- and glacier-carved valleys.

  • Estuaries age by slowly filling with sediment from the land and the sea.

  • When young, most estuaries have broad, deep basins that are always underwater (subtidal). In middle age, the build-up of sediment around the edges of the estuary creates sandflats that are sometimes underwater and sometimes exposed (intertidal) and plants begin to grow. In old age, intertidal flats colonised by mangroves cover most of the estuary, with small tidal channels carrying water from land out to sea.

  • Most of the estuaries in Aotearoa New Zealand are middle- or old-aged.

  • Estuaries are among the most productive ecosystems on earth, meaning they can grow huge amounts of plant material (up to four times more than ryegrass pasture, and 20 times more than the open ocean!).

  • The plant material in estuaries becomes food for many small invertebrates (macrofauna) and breaks down into nutritious organic matter which supports further production. When healthy, estuaries support large and complex food webs that have reach far beyond their boundaries.

Learn more 

See factsheets for more information.

Understanding estuaries Estuary types

Why they're important

Learn more about these biodiversity hotspots


Why estuaries are important

  • Estuary ecosystems have very high biodiversity; thousands of species of plants and animals live within them.

  • Some open ocean and freshwater species depend on estuaries for key parts of their life cycle, such as eels / tuna, snapper, mullet and kahawai.

  • Huge flocks of wading birds feed on the macrofauna in the sand and mudflats, with some migrating great distances to do so.

  • Estuaries provide us with many cultural, recreational and educational opportunities. Estuaries have long been places of value for Māori, who harvest kai (food), materials and rongoā (medicine) from them, and established kāinga (settlements) along their shores.

  • People gain numerous benefits from healthy estuaries that are referred to as ‘Ecosystem Services’. Some are highly visible, such as the provision of food and reduction of storm damage, whilst others are less so, such as the recycling of nutrients and regulation of climate (through storing large amounts of carbon).

  • Ecosystem services are controlled largely by the activities and interactions of the plants and animals in an estuary, known as the ecosystem processes and functions.

Learn more 

See factsheets for more information.

Understanding estuaries Estuary macrofauna Estuary types

Threats to estuaries

What we know about the pressures on these valuable environments


What are the threats to estuaries?

All estuaries in Aotearoa New Zealand are impacted by human activities, and each experiences a different combination of threats. The range of threats to estuaries include:

Upstream pressures (resulting from catchment land use)

  • Excess sediments

  • Excess nutrients

  • Contamination from land-based chemicals

Marine pressures (activities within the estuary)

  • Over-harvesting

  • Contamination from ports and marinas

  • Anchoring and dredging

  • Invasive species

Pressures at the margins

  • Reclamation

  • Livestock grazing

  • Hardening of the shoreline through development

Climate change

  • Sea level rise

  • Heat waves

  • Drought and erosion from extreme weather

Learn more 

See factsheets for more information.

Understanding estuaries

Monitoring estuaries

Most estuary monitoring is carried out by regional councils and unitary authorities, who are responsible for managing the sustainable use of natural resources in their region and have a duty to gather and record information on the State of the Environment (SOE).  Other agencies that undertake monitoring in estuaries include Fisheries NZ (fish and shellfish focus) and Department of Conservation (marine reserves focus), plus citizen science is conducted across the country.

Councils monitor estuaries to understand their ecological condition and how this is changing over time, especially in relation to human activities that may degrade their health. The monitoring results help us understand whether such activities are being managed effectively.

Three indicators of estuary health that are measured nationally by councils are presented on LAWA, these are mud content, contaminants and estuary macrofauna. Most monitoring sites are intertidal, and data are available from 2010 onwards as this constitutes the most complete and consistent national dataset (regional councils and unitary authorities may hold longer datasets for individual monitoring sites).

Mud content

Why you should care about this pressure indicator


What is mud content?

Mud content refers to the amount of fine silt and clay particles (collectively called ‘mud’) that are present in the surface layers of estuary sandflats. The mud comes from the land and has a large effect on the plants and animals living in an estuary.

How is mud content monitored?

A small corer or scoop is  used to collect sediment samples from the top 2 cm of the sandflat. Several samples (replicates) are usually collected from across the monitoring site to capture the variability of mud content. Samples are then sent to a laboratory for analysis.

On LAWA, the results are compared to custom national guidelines that show when mud content concentrations are expected to have negative impacts on the macrofaunal community. It is important to consider the location of the monitoring site within the estuary when interpreting these results. Sites at the top of the estuary are closer to the river inflows that carry the mud, and often have low tidal energy allowing more mud to settle onto the sandflat. Sites closer to the mouth of the estuary (where it joins the sea) often have higher tidal movements and may be naturally less muddy.

Learn more 

See factsheet for more information.

Mud content in Estuaries


Why you should care about this pressure indicator


What are contaminants?

'Contaminants' are any pollutants or substances that can become harmful to humans or living organisms when introduced into their environment. Contaminant monitoring in estuaries focusses on concentrations of heavy metals (such as copper, lead, zinc and cadmium) and may also include organic compounds.

Contaminants can remain in the environment for a very long time, they can bioaccumulate in some species, and at elevated levels they are toxic to aquatic life. The build-up of contaminants can affect ecological health by reducing the number and/or diversity of animals living in and on the sediment, disrupting the natural functioning of estuarine ecosystems. 

How are contaminants monitored?

Monitoring sites are generally located on intertidal sand or mudflats. A small plastic corer or scoop is used to collect the top 2 cm from a small area of sediment. As the distribution of contaminants can vary across a site, multiple samples or subsamples are often collected. Samples are analysed at a laboratory.  Heavy metail contaminants typically change relatively slowly over time, so are not sampled as frequently as other indicators such as mud content.

Monitoring results can be assessed by comparing the contaminant concentrations to sediment quality guidelines. These guidelines define low and high thresholds that indicate whether the contaminant concentrations are likely to be having negative ecological impacts.  The upper reaches of an estuary may be more contaminated than near the estuary mouth as the sheltered conditions help sediment bound contaminants settle out.

Learn more 

See factsheets for more information.

Estuary contaminants

Estuary Macrofauna

Understanding this indicator of state


What are estuary macrofauna?

Estuary macrofauna are the small animals living in estuaries that can be seen with the naked eye and do not have backbones (invertebrates). In this topic, we refer specifically to benthic, soft sediment macrofauna, i.e. those that live on and in the sand and mudflats.

There are many species of macrofauna including worms, snails, crustaceans and bivalve shellfish like cockles and pipi. They each have preferred living conditions and different sensitivities to things like mud and contaminants and are important for the functioning of the estuary.

How are macrofauna monitored?

Plastic corers (13 cm in diameter and 15 cm deep) are used to collect a section of sand or mud which is sieved over a 0.5 mm mesh to keep only the macrofauna and other larger pieces of debris (shells and stones, for example). The sample is preserved and sent to a laboratory where the different species are identified and counted to describe the macrofauna community.

The macrofauna community data are used to calculate a health indicator score (referred to as a 'Benthic Health Model').  This indicator looks at the macrofauna found at the site and compares them to other sites that sit along a known gradient of impacts from mud.  This is a useful way to summarise the health of the monitoring site, with guidelines telling us if there has been ‘very low impact’, ‘low impact’, ‘moderate impact’, ‘high impact’ or ‘very high impact’.

Learn more 

See factsheets for more information.

Estuary macrofauna

LAWA Estuary Health National Picture Summary 2023

Publish date: 22 September 2023

Welcome to the LAWA Estuary Health National Picture Summary. Here, we present information and themes about the estuary monitoring data from New Zealand's regional councils and unitary authorities at a national scale.

Estuary Health data have been collated from hundreds of monitoring sites spread across 82 different estuaries.  The data we report come from samples that are collected regularly from estuaries as part of State of the Environment monitoring.  These data help scientists and decision-makers understand the state of estuary health and track changes over time.

The 416 monitored sites listed on the LAWA website represent various estuary types, ranging in size from a few hectares to tens of thousands. Some estuaries have been monitored for one or two years and others for over three decades.  LAWA presents data from 2010 onwards, as this constitutes the most complete and consistent national dataset.  Sites in the Estuary Health topic are long-term monitoring sites so data records will grow over time.

This topic displays results for three indicators of Estuary Health that are currently monitored by regional councils and unitary authorities:

  • Mud content refers to the amount of fine silt and clay particles (collectively known as mud) that are present in the surface layers of estuary intertidal flats. It is one of the main environmental characteristics that determines where plants and animals can and cannot live within an estuary.

  • Contaminants include the metals copper (Cu), lead (Pb), zinc (Zn), cadmium (Cd), chromium (Cr), nickel (Ni), silver (Ag), mercury (Hg), arsenic (As), and organic contaminants such as hydrocarbons and pesticides.  When concentrations of these contaminants get too high, they can have negative effects on estuary health.

  • Estuary macrofauna are small invertebrates that can be seen with the naked eye and include hundreds of species of worms, snails, crustaceans, and shellfish like pipi and cockles. Macrofauna are good indicators of estuary health because the community of species found in an area represent relatively long-term, local conditions.

These indicators have been selected for the Estuary Health topic as they provide meaningful information about estuary condition and are monitored in a consistent way by regional and unitary councils across the country.  In some regions, other useful indicators are monitored including sediment nutrient concentrations, sediment organic matter, Chlorophyll a content, sedimentation rates and the extent of certain habitats.  The Estuary Health topic will be expanded as the collection of data for these and other indicators become more uniform.

Council estuary monitoring programmes are designed to give insight at a local level, so site selection is often biased towards local monitoring requirements.  The number of sites within each estuary is not necessarily proportional to the estuary's size and may depend on factors such as pollutant levels, resource availability, estuary type, and more.  More information is available on the estuary site pages, and by contacting the relevant regional council or unitary authority.  Monitoring also generally focuses on estuaries that are likely to be impacted so the estuaries monitored are not necessarily a balanced representation of all estuaries in New Zealand, and caution is advised when comparing the results on a national scale.  

However, some broad patterns can be seen in the current monitoring data.  Namely, estuaries closer to human populations and activities are muddier and more contaminated than those in less modified landscapes. Concentrations of metal contaminants are usually higher in estuaries close to cities, whereas high mud content is the biggest stressor of estuaries in rural locations.  These patterns mean estuary health can vary greatly even within regions.  For instance, Waitematā Harbour is surrounded by the largest city in the country and in places has elevated concentrations of zinc, lead, and mercury.  Further north in the Auckland region, Whangateau Estuary is surrounded by crops, grassland, and small urban areas and has very low contaminant and mud concentrations.

Estuaries are complex ecosystems that are influenced by activities happening upstream as well as out at sea.  This can make it challenging to identify and manage all of the factors that affect their health.  Additionally estuary management is complex as many agencies have overlapping roles, and it is not always clear who is responsible.  In most cases, it has taken decades of deforestation and land use change for mud and contaminants to build up, and the estuary type is also a factor in how susceptible an estuary is to the various threats. 

Restoring estuaries also takes time, and some estuaries may never return to their ‘natural’ state.  However, the dynamic nature of estuaries means if we reduce the amount of pollutants entering estuaries, they may have the potential to recover.  For example, concentrations of the contaminant lead (Pb) have decreased in many urban estuaries since the mid-1990s when it was removed from use in paints and petrol.

Explore more

You can freely explore the data through the Estuary Health topic, using the map (desktop users) to look at patterns within estuaries and regions, and the indicator figures to see how their values have changed through time.

More estuary resources are available online from LAWA and our partners to help inform and inspire. Below we have links to LAWA estuary health factsheets, the DOC Estuaries Hub, and national reporting from the Ministry for the Environment and Statistics New Zealand.

Factsheet: Understanding estuaries

Factsheet:  Estuary types

The Department of Conservation’s Estuaries Hub website is all about connecting people with each other, and with resources, to help improve the health of these special places. It has a wealth of resources developed in partnership with councils, educators, and restoration groups.

Estuary Hub

Ministry for the Environment (MfE) and Stats NZ regularly report on the state of Aotearoa New Zealand’s marine environment. Our marine environment 2022 is the latest in a series of environmental reports that includes a national overview of estuary health.

Our marine environment 2022

Stats NZ collect information to publish insights and data about New Zealand, including marine indicators that relate to estuary health.

Coastal and estuarine water quality

Heavy metal load in coastal and estuarine sediment