Out of sight, but not out of trouble: groundwater contamination in NZ reveals a legacy of human pressure

The latest official stocktake of the state of New Zealand’s freshwater carries many of the headline messages we have come to expect.

Pressures such as intensive land use and climate change are continuing to degrade our lakes, streams and rivers, with pathogen contamination making many monitored sites unsafe for swimming.

The country’s vulnerable freshwater habitats are struggling with stresses that range from nutrients and invasive species to warming water temperatures.

And once again, the Ministry for the Environment and Stats NZ’s new report, Our Freshwater 2026: Tō Tātou Wai Māori, underscores just how central freshwater systems are to our wellbeing. They support our health, help produce our food and energy, and sustain ecosystems.

What sets this latest report apart from others before it, however, is its focus on a part of the water cycle that is largely out of sight – but nonetheless crucial.

A hidden system with a long memory

Groundwater is what fills the pores and fractures of sediments and rocks beneath our feet, sometimes just a few metres down, and in other places hundreds of metres below ground.

It is core source of water for agriculture and provides drinking water to nearly half the population. During dry periods, it maintains the flow of rivers by slowly releasing water stored in aquifers.

Groundwater can also act as both a sink and a pathway for contamination. Once nutrients and other pollutants enter groundwater systems, they can linger within them for years, and often decades, before reemerging.

Today, groundwater sampling is showing the legacy of generations of human influence on New Zealand’s landscapes.

The report indicates that levels of nitrate – a form of nitrogen typically stemming from fertiliser use and livestock waste – have been increasing at 39% of monitored groundwater sites around the country, while declining at just 26% of sites.

Around 43% of monitored sites had nitrate levels above natural reference ranges – the levels expected without human influence – further pointing to the impact of activities such as farming.

Particularly where groundwater is shallow or poorly protected, contamination from land use has been affecting drinking water supplies.

Between 2019 and 2024, for instance, 45% of monitored groundwater sites recorded levels of the harmful bacteria E. coli above safe drinking water limits at least once – and 12% exceeded thresholds for nitrate.

Lag-times and blind spots

As the report acknowledges, groundwater doesn’t move in simple or predictable ways.

We often hear freshwater scientists speak about “lag-times”. This is effectively the time taken from a contaminant leaving a farmer’s paddock and later appearing in a drinking water supply.

In reality, groundwater transport processes remain poorly understood. These can vary across the country – and even within individual catchments – depending on factors such as soil, geology, depth and proximity to rivers.

In some cases – particularly where water is able to move quickly through soils during heavy rainfall – contamination linked to human activity can show up in groundwater within days to a few years.

In Canterbury, for instance, shifts in nitrate concentrations have emerged in spring-fed streams and shallow wells within five years of land use intensifying nearby.

But in other parts of the system, contaminants can take much longer to turn up and flush out. Understanding these differences is important, because we risk misreading long-term trends and missing where – and when – problems are actually occurring.

At the same time, much of what is happening below the surface remains difficult for scientists to track. Standard monitoring approaches used today can miss short-lived spikes after storms, which can obscure how much contamination is present, or whether it is driven by rainfall or ongoing land use.

New low-cost nitrate-tracking tools are helping to untangle this picture, revealing just how much contamination levels in New Zealand’s groundwater can fluctuate over time.

In some cases, during wetter periods when groundwater systems naturally recharge, nitrate concentrations in monitoring wells have been observed to surge from minimal levels to those well above safe drinking water limits.

By capturing this variability through more targeted, high-resolution monitoring, we can more clearly see how contaminants move through groundwater systems. These tools also make standard spot samples collected by regional councils far more useful, helping distinguish short-term surges from longer-term pressures.

More broadly, there are other challenges to confront. Freshwater data is often fragmented across different organisations and important knowledge – including mātauranga Māori – remains often underused in resource management.

Ultimately, all these gaps limit our ability to build a clear, complete picture of what is happening within our waterways, both below and above the surface.

From resource to risk?

Just as importantly, the report notes that pollution from land use isn’t the only pressure now facing groundwater. In some places, particularly low-lying coastal areas, groundwater itself is becoming a hazard.

As sea levels rise, groundwater levels are likely to be pushed higher, both near the coast and further inland. This raises the risk of flooding, liquefaction and damage to infrastructure.

Rising sea levels and other climate change impacts can also bring saltwater into coastal aquifers, making groundwater less suitable to use, while affecting underground assets such as pipes.

Such vulnerabilities underscore the report’s central theme: that water availability and water quality pressures are shifting, driven by climate change, land use and coastal processes.

Meeting that challenge will require a clearer understanding of the whole system – closing critical knowledge gaps and making better use of the tools and data already available.