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Pūtaiao wainuku

Groundwater science

Forty percent of Aotearoa relies on groundwater for drinking, but it’s vulnerable to contamination and increasingly threatened by land use and climate change. ESR science is exploring how we can protect this valuable resource for the benefit of every New Zealander.



Groundwater is stored underground in spaces between rocks or soil and is an important source for replenishing surface water and drinking water. Almost half of the population in Aotearoa New Zealand rely on groundwater for drinking, but it’s vulnerable to contamination. ESR is working to ensure groundwater is safe and resilient to future challenges.

The majority of monitored groundwater resources don’t meet standards. What’s more, groundwater resources are increasingly threatened by factors like land-use change and climate change. All of this reduces the health of groundwater ecosystems, and therefore the overall status of our freshwater ecosystems.

Access to safe water is a fundamental human right. Through an in-depth, research driven understanding of groundwater contamination processes, our groundwater scientists help clients to identify and address issues associated with land use intensification and its effects on groundwater quality. 

We also design tools for water managers to enable them to assess, predict and minimise the impacts of climate change and land use on groundwater quality.

Groundwater management

Groundwater management

Through an in-depth, research driven understanding of groundwater contamination processes, our team of groundwater scientists help clients to identify and address issues associated with land use intensification and its effects on groundwater quality.

We also design tools for water managers to enable them to assess, predict and minimise the impacts of land use, and land use changes, on groundwater quality.

Our research

He Wai Māpuna

Our groundwater scientists are working with Rūnanga o Ngāi te Rangi and Ngā Hapū o Matakana me Rangiwaea as part of ESR's He Wai Māpuna programme. They're developing a wai programme for Matakana whānau that will include groundwater visualisations and groundwater monitoring on Matakana Island.

Groundwater health index

We're busy establishing a groundwater health index focused on the presence of macroinvertebrates in groundwater and microbial diversity.

Active involvement with regional and district councils

We have active involvement with regional and district councils throughout New Zealand, providing advice, exchange of hydrogeological data, and undertaking research and case studies of concern and importance to councils.

A recent request from all the councils was to develop a tool to assess the risk of microbial contamination to drinking water supply wells from a range of land uses. This was funded from an Envirolink Tools grant and was carried out jointly with GNS Science.

Pacific consultancy

We're contributing knowledge and design concepts for future public health programmes with and for countries in the Pacific region (from policy to practice). The goal is to empower them to achieve their goals for cleaner, safer drinking water and sanitation.


We have co-ordinated national survey of pesticides in groundwater every 4 years since 1990 for the regional councils. The last two surveys have included a suite of emerging organic contaminants (EOCs).

Groundwater modelling

Groundwater modelling

ESR’s data scientists are helping to build a picture of how contaminants and pathogens survive and move through our groundwater systems and the impact this has on the quality and safety of the water we use.

Groundwater is one of Aotearoa New Zealand’s most valuable resources. It provides drinking water to 40% of the population, more than 30% of the water for the primary sector (such as farming and forestry), and a massive 80% of New Zealand’s springs, streams, and wetland baseflows.

At the same time, the impact of climate change, changing land use, and chemical pollutants are putting the safety and quality of our groundwater at risk. To build understanding of how contaminants move into and through aquifers, and how those contaminants are naturally filtered or bioremediated, ESR’s scientists carry out large scale field experiments and analyse the results using a combination of data science and numerical modelling.

Our groundwater modellers analyse pathogen, tracer, and nutrient experimental datasets alongside real-time groundwater sensor data from ESR’s experimental sites in Canterbury and sites across New Zealand. The team is also developing a set of visualisation tools to better demonstrate to our communities the outcomes of their work, how groundwater moves through aquifers, and how different contamination sources degrade the quality and safety of groundwater supplies and freshwater bodies.


Pathogen and nutrient movement in different groundwater systems

The team will use novel synthetic surrogates and DNA tracers to identify the pathways and processes that harmful microbes and contaminants take in aquifers.

In one experiment, the DNA tracers will be simultaneously injected at several wells at ESR’s Canterbury testing site and their movement will be tracked with very intense sampling.

The sampling results will be analysed numerically in 3D space and time. By mapping the movement of these synthetic tracers, the team will be able to better predict how contaminants are transported through groundwater systems.

Merging Machine Learning and numerical tools

Regional councils know that carefully-mapped drinking well capture zones (the area around a drinking water well that contributes water, and potentially contaminants and pathogens,  to the well) are essential to minimise public health risks and the economic impact on farmers. But building a picture of the complex geological structures under the ground is difficult.

To address this, ESR scientists are developing efficient new methods to simulate well source protection zones, combining novel hybrid deep learning and numerical architectures.


On-site Wastewater Management Systems (OWMS)

On-site wastewater management systems, previously called septic tanks, treat and dispose of sewage into the environment in places that aren’t connected to reticulated wastewater infrastructure (the main sewerage system).

ESR is working closely with regional councils and the on-site wastewater industry to assess the impact of on-site wastewater management systems on our public health and the environment, in particular groundwater quality. Understanding the impact this type of wastewater management has on our groundwater quality is vital – especially when that groundwater is used for drinking water.

Our research


ESR scientists are helping councils throughout Aotearoa in four main research areas:

  1. Estimation of number and location

    Canterbury-based ESR scientists, along with Environment Canterbury (ECan), are investigating how Geographical Information Systems (GIS) can be used to estimate the number and location of unknown on-site wastewater management systems. This will help with future risk assessments and resource management planning decisions at a regional and national level.

  2. Typical on-site wastewater management systems wastewater quality

    ESR and ECan are surveying thirty on-site wastewater management systems(of varying designs, ages, capacities and household occupancy) across Canterbury to determine their chemical and microbiological composition, as well as the presence of Emerging Organic Contaminants (EOCs).

  3. Impact on groundwater quality

    ESR scientists are also monitoring groundwater quality a domestic on-site wastewater management systems at a field research facility in Canterbury in collaboration with ECan, Hynds, and industry specialists. This research will help guide efforts to improve on-site wastewater operation, maintenance and treatment, and measure the microbial and chemical contribution of the on-site wastewater management systems to the receiving environment.

  4. Climate change implications

    At the on-site wastewater management systems research facility we're exploring how fluctuating groundwater levels caused by climate change affect this on-site wastewater management systems and potential groundwater contamination.

Why it matters

New Zealand councils are aware of where consented On-site wastewater management systems are located, but for systems that pre-date resource consent requirements (pre-2000), the location and number of on-site wastewater management systems in a region is often unknown. This creates issues when risk assessments for drinking water supplies are completed, particularly when that drinking water source uses groundwater in an area heavily serviced by on-site wastewater management systems.

There is also not enough research to determine the impact of these systems on groundwater quality and the quality of the wastewater itself for a New Zealand context. New Zealand councils and engineers typically rely on international data to estimate the wastewater quality and risks from on-site wastewater management systems on the surrounding environment and human health. But using international data is problematic because these data are collected from on-site wastewater management systems with different designs, standards, climatic conditions, and therefore different treatment capacities and discharge quality, than those commonly used in Aotearoa.

The impact of climate change

Our changing climate makes this research even more important. From droughts to intense rainfall, New Zealand is experiencing an increased frequency of extreme weather events, resulting in rapidly fluctuating groundwater levels. This increases the potential for groundwater to mix with on-site wastewater, which is a risk to groundwater drinking water sources.

Project leader Dr. Louise Weaver says: "Instead of a ‘flush and forget’ mentality, ESR is helping to shine a light on the risks associated with on-site wastewater so that our communities and environment are protected and treasured as a taonga.

Find out more

For more information about the research, contact Louise Weaver (science leader) or Bronwyn Humphries (project lead).

For more information about onsite wastewater management systems, check out ECan’s wastewater information.

Contaminants in groundwater

Contaminants in groundwater

ESR carries out a national assessment of contaminants in groundwater every four years.

The four year survey is for district and regional councils, to assess the quality of their groundwater resources. Samples are taken from approximately 165 wells and tested for a range of over 80 pesticides. ESR has been coordinating this groundwater survey since 1990.

ESR also undertake more general, ‘on-request’ assessments of regional groundwater quality for councils.



The 2018 survey tested for glyphosate for the first time, along with a number of Emerging Organic Contaminants (EOCs). Glyphosate is the active ingredient in a popular weed killer.

Glyphosate was only found in one well from the 135 wells tested – and the level detected was well below (over 400 times lower) WHO recommended health-based value.

“The majority of the wells in the survey showed no change in the amount of pesticides present compared to previous surveys, with less than a quarter of the wells having low levels of pesticides detected,” said ESR principle scientist Murray Close.

“None of the sampled wells exceeded safe drinking water standards, with most pesticides detected at less than 0.5% of the maximum acceptable value (MAV).”

Emerging organic contaminants (EOCs)

Wells were also tested for a range of emerging organic contaminants (EOCs) using a highly sensitive analytical technique that measures EOCs at extremely low concentrations (parts per trillion). The survey tested for close to 30 of these compounds including a diverse range of products such as caffeine and artificial sweeteners along with pharmaceuticals such as pain relief products, contraceptive pills and sunscreen.

“We found these compounds in 70 per cent of wells and detected 25 of the 29 compounds we tested for.”

Overseas research links the discovery of EOCs in groundwater to wastewater sources, including municipal treatment plants, septic tanks, farming activities, as well as indirectly from surface water.

Murray Close says there are no known health or environmental risks, however there are generally no health guidelines associated with EOCs. "The contaminants are widely used and do make their way into the environment in low concentrations.”

The survey recommends that monitoring of groundwater resources is extended and that research is carried out to investigate the likely risks for the EOCs detected in this study including any impacts on ecological systems.

Per- and Polyfluoroalkyl Substances (PFAS)

The EPA commissioned the tests for PFAS in 2022, as part of the Institute of Environmental Science and Research (ESR) four-yearly survey of pesticides in groundwater.

Bioremediation of Groundwater

Bioremediation of groundwater

ESR is developing new methods for the removal of nitrogen from groundwater systems.

New Zealand’s alluvial aquifers in Canterbury, Hawkes Bay, Wairarapa, Southland, Waimea and Marlborough supply irrigation water to large, highly productive farming areas. However, the enhanced production also increases the use of fertiliser and the amount of animal waste that is generated. The nitrogen from these products washes straight through the alluvial soils, into the aquifers, which have little capacity to reduce the nitrates. These aquifers feed lakes and rivers, putting ever increasing quantities of nitrates into the environments loved by New Zealanders.

This tension between farming needs and the environment is increasing, making it likely that production will be constrained in many areas such as Canterbury and the Hawkes Bay.

Finding an innovative solution

Alluvial aquifers

Alluvial aquifers are characterised by fast and heterogeneous groundwater flow patterns, which makes it very challenging to develop, design and implement remediation options. Our research is instead looking at creating conditions in fast-flowing alluvial aquifiers that will bring about denitrification.

Denitrifying Permeable Reactive Barriers (PRB)

ESR is developing innovative approaches such as denitrifying Permeable Reactive Barriers (PRB). We use advanced shallow depth geophysics, DNA tracers and groundwater microbial community analysis to characterise the aquifer and effectively design and implement mitigation tools like this.

Denitrifying bioreactors

Another technology being trialed is the use of denitrifying bioreactors to treat nitrate from artificial drains. An instream bioreactor using woodchips is being installed near the end of a drainage system that collects shallow groundwater in the Barkers Creek catchment, South Canterbury.

The bioreactor stimulates denitrification and reduces the nitrate before it enters Barkers Creek. Denitrification walls are a tried and tested concept in slow moving sandy aquifer systems where they have proven effective at treating nitrate from point pollution sources. There are no examples, however, of these remediation systems having been installed in gravel aquifers such as those found in Canterbury. In this regard, ESR's pilot study represents a world-first. 

Why it matters

These new methods for on-farm denitrification will enable more sustainable farming systems. It is estimated that bioreactor technology can reduce nitrogen by a significant proportion annually.

The research team

Our current research team includes people from ESR and Southern Geophysical, and the previous related project also included collaboration with Lincoln Agritech, Aqualinc Research, and University of Canterbury.

Ngāi Tahu Farming and Environment Canterbury have been involved in proposal development and field site selection and actively monitor progress and results.

Groundwater Science and Research Alliance Aotearoa

ESR, along with groundwater scientists at GNS ScienceAqualinc and Lincoln Agritech also work together, building on each other’s strengths, to improve the understanding and quality of groundwater research. This is called the Groundwater Science and Research Alliance Aotearoa.