Understanding the Groundwater Ecosystem

By understanding the role of key organisms in aquifer ecosystems, scientists from ESR and Auckland University are developing a groundwater health index to help manage and protect this taonga. 

Groundwater is a vital taonga that supplies 80% of water into Aotearoa New Zealand’s rivers and streams and 40% of our drinking water. The perception is that groundwater is a sterile environment, but in reality, underground microbes support a complex ecosystem that keeps the groundwater clean and healthy by processing contaminants such as nitrates.

However, these natural underground communities of organisms are under threat due to the volume and cumulative effects of contaminants coming from land use, not to mention increasing climate stress affecting the whole water cycle. In fact, there is still much to learn about groundwater organisms and their functions in removing contaminants, and the emerging stressors on their ecosystem.

The Groundwater Health Index (GHI)

Researchers from ESR and Auckland University are studying the organisms that exist in underground aquifers to understand their roles and responses to contaminants, and developing an index that indicates the groundwater ecosystem’s health. The scientists are also building a picture of the stresses the groundwater environment is under, and by tracking the changes in biological diversity, they can monitor water quality.

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Tasman District Council Resource Scientist Joseph Thomas and ESR Science Leader Louise Weaver sample groundwater, Golden Bay.

ESR science leader Dr Louise Weaver says changes in above-ground ecosystems are well understood because they have been studied intensively for so long. “Take for example the African Plains – we know what the lions and zebras do and how they interact. By comparison some of the macroinvertebrates and microorganisms in groundwater systems have yet to be identified, let alone understand their interactions.”

Louise says one of the challenges has been identifying the organisms that play a part in removing nitrates in groundwater. This project has developed and is refining sampling methodologies using specialised techniques. For example, larger macroinvertebrates can be captured using nets, while smaller organisms require pumping large volumes of water from the ground, filtering, and extracting eDNA (environmental DNA) to identify what is present.

The researchers are using this information to create a useable database to help understand regional differences in groundwater systems and detect new organisms, from microbes through to macrofauna living in groundwater.


Aside from the inherent conservation value in the array of organisms present in groundwater, this research could also lead to bio-remediation techniques. By understanding the processes and organisms involved, in the future it may be possible to introduce some of these organisms into the system to enhance bio-remediation processes and improve groundwater quality.

This new Groundwater Health Index is aiming to become a practicable tool for predicting the health of groundwater and monitoring the stresses and changes to this vital yet hidden ecosystem.

For more information contact Dr Louise Weaver