Factsheet: Estuary contaminants

What are estuary contaminants?

Contaminants are any pollutants or substances that can become harmful to humans or living organisms when introduced into their environment. A range of different contaminants can be monitored in estuaries and generally fall into two broad categories – metals and organic contaminants.

Many metals and organic compounds occur naturally in the environment, and trace amounts of some metals (such as copper and zinc) are even essential for natural processes, enabling plants and animals to grow and reproduce. However, human activities can cause concentrations to be much higher than would be expected naturally such that they become harmful contaminants. Contaminants may enter estuaries through stormwater networks, rivers, or be discharged directly into them.

Commonly monitored metals include copper (Cu), lead (Pb), and zinc (Zn) (the main contaminants associated with input from urban stormwater), along with arsenic (As), mercury (Hg), cadmium (Cd), chromium (Cr) and nickel (Ni) (which are usually associated with rural land practices). Sources and concentrations of metals will vary depending on the land use and activities occurring in and around an estuary. Natural sources, such as geothermal activity or the weathering of rocks, can also play a role.

Organic contaminants include polycyclic aromatic hydrocarbons (PAHs) and dichloro-diphenyl-trichloroethane (more commonly known as DDT). PAHs are derived from fossil fuels and are present in oil, coal, and tar. Background levels of PAHs can be found naturally in the environment from events such as forest fires and volcanic activity, but concentrations can be elevated when contributions from urban sources such as vehicle exhaust emissions or oil spills occur. DDT was a commonly used insecticide for many decades in Aotearoa New Zealand. It is now a legacy contaminant (meaning it is no longer legally used) and as a result levels should decrease over time.

There are also new pollutants entering our estuaries. These include a very broad range of chemicals and substances that are not yet routinely monitored but have the potential to cause negative ecological or human health effects, such as microplastics and chemicals from personal hygiene products. For many of these pollutants, known as ‘emerging contaminants’, their fate, toxicity, and effects are largely unknown. Outcomes of national research will help to guide future directions in emerging contaminant monitoring.

Why monitor estuary contaminants?

Contaminants can build up in the sand and mudflats of estuaries and are generally environmentally persistent, meaning they can remain in the environment for a long time. At elevated levels contaminants are toxic to plants and animals, and some may also bioaccumulate. One of the consequences of this are that the number and diversity of macrofauna living in the sediment is reduced, leaving degraded communities that are dominated by a few tolerant species, and there are declines in the ecological condition of the estuary.

Monitoring the concentration and distribution of contaminants in estuary sediments helps us to understand their potential effects on benthic ecology and provides information on how different land uses and human activities impact estuaries.

How are estuary contaminants monitored?

A small corer or flat-bottomed scoop is used to sample the top 2 cm of sediment from estuary sandflats for contaminant analysis. This provides an integrated mix of some freshly deposited material, along with slightly older, deeper sediment. The distribution of contaminants can vary across a site, so often multiple samples are collected (known as replicates), or samples are made up of multiple sub-samples (known as a composite sample). Samples are kept cold or frozen (this stops any biological activity from occurring that may alter contaminant levels) before being submitted to a laboratory for analysis. Contaminant concentrations can be analysed using either the whole sediment sample, or a fraction of the sediment that has been sieved to remove larger particles (greater than 0.5 mm).

When measuring organic contaminants, it is also necessary to measure the amount of total organic carbon (TOC) in the sediment. This is because organic matter can help bind organic contaminants to the sediment and influences overall concentrations. TOC is therefore used for calculating organic contaminant concentrations in a way that allows comparisons with sediment quality guidelines.

When choosing where to monitor contaminants it is important to consider that local estuary dynamics can influence contaminant concentrations. Muddy, low energy areas are prone to trapping and accumulating contaminants and generally have higher concentrations of metals compared to sandier, more exposed sites with higher wave or tidal energy. Having a spread of monitoring sites along an estuary can help us see and understand these patterns.

How are contaminant results assessed?

Contaminant concentrations can be assessed by comparing monitoring results with sediment quality guidelines. These guidelines have been derived from a range of studies using both field ecology and laboratory ecotoxicity-effects data. These data are used to develop thresholds to indicate when contaminant concentrations have the potential to cause negative ecological effects. Generally, guidelines follow a tiered approach using low and high concentration thresholds. Concentrations below the low threshold values reflect a relatively low level of contamination where minimal impact on ecology is expected, interim concentrations between low and high thresholds indicate moderately elevated levels where negative effects on ecology may be beginning to appear, and concentrations above the high threshold indicate levels of contamination where ecological degradation is likely to be occurring  

The guidelines commonly used and available for comparison on LAWA include:

  • The Australian and New Zealand guidelines for fresh and marine water quality (ANZG).
  • The Threshold Effect Level (TEL), and the Effects Range Low (ERL).
  • The Environmental Response Criteria (ERC).

The TEL, ERL and ERC approaches are generally more conservative than the ANZG guidelines and use lower contaminant thresholds, providing an earlier warning of environmental degradation, allowing time for further investigations to take place and mitigating measures to be introduced before further degradation can occur.


Read more

ANZG. (2018). Australian and New Zealand Guidelines for Fresh and Marine Water Quality, Australian and New Zealand Governments and Australian state and territory governments, Canberra ACT, Australia.

Auckland Regional Council. (2004). Blueprint for monitoring urban receiving environments. Technical publication no. 168 revised edition.

Long, E.R., Macdonald, D.D., Smith, S.L. et al. (1995) Incidence of adverse biological effects within ranges of chemical concentrations in marine and estuarine sediments. Environmental Management 19, 81–97. https://doi.org/10.1007/BF02472006

MacDonald, D., Ingersoll, C. & Berger, T. (2000). Development and Evaluation of Consensus-Based Sediment Quality Guidelines for Freshwater Ecosystems. Archives of Environmental Contamination and Toxicology 39, 20–31. https://doi.org/10.1007/s002440010075