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Estuary Health

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

Healthy estuaries support a wide variery of plants and animals and are highly valuable ecologically. 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 maintaining water quality by naturally filtering water and binding pollutants within sediment. When we look after estuaries, they look after us.

In this topic, you can learn more about why estuaries are so important, the biggest threats to their health. and explore monitoring data from estuaries around New Zealand, including a national summary 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

Overview

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

Overview

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

Overview

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

Overview

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

Contaminants

Why you should care about this pressure indicator

Overview

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

Overview

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 2025

Published: 28 September 2025

 

 

Why estuaries matter

Healthy estuaries are home to 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.

 

What is monitored and shown on LAWA?

We present information 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 across 104 different estuaries (around one-third of all estuaries in the country). This year, estuaries in Gisborne are included for the first time. The data we report comes from regular sampling as part of State of the Environment monitoring programmes. These data help scientists and decision-makers understand estuary health and track changes over time.

The 442 monitored sites listed on the LAWA website represent a wide variety of estuary types, ranging in size from a few hectares to tens of thousands. Some estuaries have been monitored for one or two years, while others have records from over three decades. LAWA presents data from 2010 onwards, as this marks the most complete and consistent national dataset. The Estuary Health topic focuses on long-term monitoring sites, with data records that will continue to grow over time.

This topic includes results for key indicators of estuary health, 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. Mud content is a key environmental factor that influences 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), as well as organic contaminants like hydrocarbons and pesticides. When present at high concentrations, these substances can negatively effect estuary health.

  • Estuary macrofauna are small invertebrates visible to 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 invertebrates found in an area reflect long-term, local environmental conditions.

These indicators have been selected for the Estuary Health topic as they provide meaningful insights into estuary condition and are monitored consistently across the country. In some regions, councils also track other useful indicators such as sediment nutrient concentrations, sediment organic matter, chlorophyll a, sedimentation rates, and the extent of certain habitats. 

Council estuary monitoring programmes are designed to give insight at a local level, so site selection is often biased towards local monitoring requirements. As a result, caution is advised when comparing the results on a national scale. The number of monitoring 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. 

 

Estuary health current state

Monitoring data reveal some broad patterns about New Zealand’s estuaries:

  • Estuaries near cities and towns tend to be muddier and more contaminated than those in less modified areas.

  • Metal contaminants are typically found in higher concentrations in estuaries close to cities.

  • High mud content is generally the biggest stressor of estuaries in rural areas.

Estuary health can vary greatly, even within the same region. For example, Waitematā Harbour is surrounded by the country’s largest city, and has elevated concentrations of zinc, lead, and mercury in some areas. Further north in the Auckland region, Whangateau Harbour is surrounded by crops, grassland, and small urban areas and has very low levels of both contaminants and mud.

To give a snapshot of the current condition of monitored estuaries, summary statistics were calculated based on the latest available data for each site, focusing on two indicators: estuary macrofauna score and mud content.

The estuary macrofauna score assesses the health of monitored sites and tells us how relatively impacted the macrofaunal community is by mud, the main stressor of estuaries across the country. According to these scores: 

  • 14% (33 sites) experienced ‘low’ or ‘very low’ impacts from mud

  • 86% (198 sites) experienced at least ‘moderate’ impacts (Figure 1)

 

Estuary macrofauna score

Figure 1. The latest estuary macrofauna scores for 231 estuary sites with suitable data available.

 

 

The amount of mud at monitoring sites ranged from 0% to 98.5%. Most sites had concentrations in the 10–30% range, closely followed by those in the 30–60% range (Figure 2).

 

Mud content
 

Figure 2. The latest mud content data for 441 estuary sites.

 

Five contaminants were sampled at more than 80% of estuary sites across the country: copper, lead, zinc, arsenic and mercury. Concentrations of these contaminants were below the Default Guideline Value (DGV) from the Australian and New Zealand guidelines for Fresh and Marine Water Quality (ANZG) at most sites, most of the time. Only 41 sites (approximately 11%) had concentrations of at least one of these contaminants that exceeded the DGV, placing them in the ‘amber’ category, meaning concentrations were high enough to possibly cause ecological impacts. No sites had contaminant levels that triggered the ‘red’ category under the ANZG, where ecological impacts are considered probable.

 

Estuary health monitoring and reporting

Estuaries are complex ecosystems, influenced by both land-based activities upstream and marine processes offshore. This makes it challenging to identify and manage all 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 many cases, it has taken decades of deforestation, development and land use changes 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 takes time, and some estuaries may never return to their ‘natural’ state. However, the dynamic nature of estuaries means if we reduce the volume of pollutants entering them, they may have the potential to recover. For example, contaminant lead (Pb) concentrations have decreased in many urban estuaries since the mid-1990s, following the removal of lead from use in paints and petrol.


The Estuary Health topic will be expanded as the collection of data for additional indicators becomes more consistent across the country. Recent and ongoing work by the Ministry for the Environment to stocktake environmental attributes, collate advice on estuary indicators for Aotearoa New Zealand, and revise the National Estuary Monitoring Protocol, will support this growth.

 

Explore more

You can explore estuary health data through the Estuary Health topic. Use the interactive map (on desktop) to investigate patterns within estuaries and regions, and view indicator graphs to see how values have changed over time.


A range of additional resources is available online through LAWA and our partner organisations to help inform and inspire.

Factsheet: Understanding estuaries

Factsheet:  Estuary types

 

The Department of Conservation’s Estuaries Hub connects people with each other and with resources to help improve estuary health. It offers a wide range 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 2025

 

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