Deep groundwater has re-emerged not just as a subject of scientific interest, but as a potential game changer in addressing water security, climate, and energy challenges. Globally, new frameworks are reshaping how we understand the water cycle, particularly the vast, ancient groundwater systems lying beneath the Earth’s surface.

Research into this so-called “hidden hydro geosphere” is challenging long-held assumptions that all groundwater eventually discharges to rivers, lakes, or oceans. These deep, often saline, and isolated waters, some dating back hundreds of millions of years, are untouched by modern recharge and may lose life adapted to extreme conditions. They also contribute to geochemical cycles and contain critical resources like helium, hydrogen, and lithium, increasingly vital to the global energy transition. As interest in carbon sequestration, radioactive waste disposal, and deep subsurface exploration grows, so too does the need to understand the rates and processes that govern these ancient (fossil formation) water systems.

But for all its promise, this hidden hydro geosphere is also a potential Pandora’s box. Tapping into it without a clear understanding could risk contamination, irreversible changes to deep geological systems, or long-term environmental damage. What we do not know about deep groundwater may prove just as dangerous as what we do.

Pandora’s box

This is where the use of multiple tracers, both environmental and artificial, becomes necessary. Just as oceanographers have long used the concept of residence time for different dissolved components to understand ocean circulation, hydrogeologists are now adopting similar approaches to decipher the complex age structure of groundwater systems.

Ages derived from physical flow models often differ from those derived chemically, and integrating these perspectives allows for more robust interpretations. Environmental tracers, including stable isotopes, radiocarbon, tritium, and noble gases, allow us to identify not only the “mean” age of a groundwater body but also its youngest and oldest components. It is often the youngest drop, not the average age of groundwater, that holds the key to understanding an aquifer’s vulnerability.

Even so called ancient and safe aquifers may be at risk if young, potentially contaminated water is able to infiltrate through protective layers like the vadose zone and reach deeper groundwater systems. Conversely, noble gas isotopes such as ⁴He, ²¹Ne, and ¹²⁹Xe have revealed the presence of billion-year-old water in systems like Kidd Creek in Canada and Moab Khotsong in South Africa’s Witwatersrand Basin, offering a rare glimpse into Earth’s deep geologic past and even its prebiotic condition.

This global conversation is particularly relevant to South Africa, where deep groundwater is typically defined as anything deeper than 100 to 300 meters. Despite this shallow definition compared to international contexts, we know surprisingly little about the nature, quality, and flow dynamics of these deeper zones let alone those at kilometre depths. This knowledge gap has major implications in a water-scarce country where pressures on surface water and shallow aquifers are intensifying.

In this context, understanding deep groundwater should not be seen as a mere academic exercise but essential for national planning and policy. Deep aquifers could serve as strategic reserves during prolonged droughts, augment water supplies for remote or industrial regions, or support low-carbon geothermal energy systems. They also pose legal and regulatory challenges that South Africa’s water governance frameworks must begin to anticipate.

Deep drilling

While mines in South Africa particularly gold, platinum, and chromium operations often reach depths of one kilometer or more, these mines are typically governed by strict commercial and operational confidentiality. As a result, accessing such sites for independent scientific study can be challenging, limiting opportunities for hydrogeological research at depth.

That is what makes a recent deep drilling initiative into the Bushveld Igneous Complex (BIC) particularly significant. Unlike mining driven access, a WRC funded project, conducted by Stellenbosch University, was structured specifically for hydrogeological research. The initiative drilled to depths of 950 m and successfully characterised deep, fracture-controlled aquifers within the eastern limb of the BIC. Groundwater inflows between 800 and 950 m were observed, with geophysical logging and borehole imaging confirming the role of dykes and faults as conduits for structurally controlled flow.

The shift from calcium magnesium bicarbonate (Ca-Mg-HCO₃) waters in shallow zones to sodium chloride (Na-Cl) dominated waters at depth indicates long residence times and mineral rich, isolated systems. The data also suggests that shallow and deep aquifers are likely to disconnect a key finding for groundwater protection. What makes this borehole even more valuable is that it is being preserved for future tracer studies, including noble gas analysis once conditions stabilise. Interestingly, drilling also revealed methane and other gases, even dark, odorous fluids hinting at deeper geothermal or abiogenic processes. These surprises raise new questions about gas migration, fluid pathways, and heat flow in one of the world’s largest layered intrusions.

Without such scientific baselines, policymakers may be flying blind. While the research only captured a snapshot of what lies below, it provides the first formal hydrogeological characterisation of deep fractured aquifers within the Bushveld Complex and establishes a foundation for future research, including groundwater resource assessments, geothermal energy exploration, and improved geological conceptual models. What is more, this opens the possibility of strategically deploying multiple tracers in future deep boreholes across the region not only to assess recharge dynamics and mixing processes but also to define the vulnerability of these systems to anthropogenic activity.

The integration of tracer data makes it possible to identify not just average groundwater ages, but also the critical youngest and oldest fluid components. Understanding this age structure is crucial for evaluating the feasibility and long-term safety of initiatives such as deep waste repositories, hydrogen extraction, and investigations into the deep biosphere.

If South Africa is to meet its water and energy goals under the National Water Resource Strategy or align with the Sustainable Development Goals (SDGs), deep groundwater research must move from the margins to the mainstream. Scientific evidence from projects like these can help refine licensing, prioritise areas for strategic reserve development, and set more realistic protection zones for vulnerable aquifers.

The BIC, long known for its mineral wealth, is now revealing insights about deep groundwater storage, flow, and connectivity in fractured rock settings that might reshape how we define “secure” water sources in the decades ahead. Whether these sources are a hidden asset or a Pandora’s box may well depend on how effectively we use our tracer tools to look closely into their complex past and how wisely we act to preserve their uncertain future.

By Yazeed van Wyk, research manager, WRC