Potatoes and intensive farming: A slow-moving threat to Malta’s groundwater

In certain regions of Malta, the natural water reserves stored deep underground already contain nitrate levels two to four times higher than international safety limits, driven largely by intensive potato cultivation and high-input vegetable farming.

According to a major report published in the Journal of Hydrology: Regional Studies (2026), these crops pose the greatest threat to groundwater sustainability, while orchards show far lower impacts.

The study warns that the rest of the island’s groundwater faces a similar fate as a massive build-up of agricultural pollutants migrates through the rock—a process the authors conclude makes further contamination “merely a matter of time”.

This five-year study was conducted by a team of experts including Luca Laudi, Ofer Dahan, Manuel Sapiano, Michael Schembri, Luke Galea, Ella Busuttil, John Mangion, and Tuvia Turkeltaub, representing both Ben-Gurion University of the Negev and Malta’s Energy and Water Agency.

The underground ‘storage tank’

The research focused on the vadose zone, which is the layer of soil and limestone rock that sits between the ground surface and the water table. To laypeople, this is the island’s ‘underground filter’, but the report describes it as a significant storage zone for pollutants.

Using 16 specialised monitoring stations, the researchers tracked how nitrogen from fertilizers moves through this layer. Because Malta’s rock layers can be over 200 metres thick, it can take decades for surface pollution to reach the actual water supply.

High-risk crops: potatoes and vegetables

By mapping farming practices, the report identifies specific crops that dominate nitrate pollution. The author’s state: “Potato cultivation produces the highest VZ [vadose zone] nitrate storage and is the dominant source of nitrate loading to the Mean Sea Level Aquifer (MSLA), while intensive vegetable and greenhouse farming create local contamination hotspots above the Blue Clay and Coastal aquifers.”

Potato fields showed the highest average nitrate build-up in the rock, measured at 967 mg/L. This is largely due to “one-time” fertilization at the start of the season; if heavy rain occurs, the fertilizer is washed deep into the rock before the plants can use it. This crop is the primary source of pollution for the MSLA, Malta’s most critical source of public water.

Intensive vegetable and greenhouse farming heavily impact the shallower Coastal and Blue Clay aquifers. These crops are irrigated year-round and receive the highest doses of fertilizer—roughly 439kg of nitrogen per hectare. This constant watering creates a rapid downward flow, pushing nitrates quickly into the water.

In contrast, the report highlights orchards and vineyards as far more sustainable options. Orchards, mostly dedicated to peach production, show significantly lower nitrate build-up in the underground filter layer.

Implication on water quality

The implications on health are stark. In the eastern areas of the main aquifer, the report notes: “Specifically, the highest concentrations of nitrate are observed in the eastern areas of the MSLA, ranging from 100 to 200 mg/L.” This is two to four times higher than the EU safety limit of 50 mg/L. The EU has safety limits on nitrates to protect public health and freshwater ecosystems. Nitrates are safe at low levels but become harmful when concentrations rise due to agricultural runoff and fertilisers.

Describing groundwater as the “primary natural freshwater resource” for Malta, the report notes that contamination poses “significant risks” to its availability. The presence of these high nitrate levels is described as a “major threat to the aquifer’s water quality”.

A new framework for management

This study provides a practical map for identifying non-point sources of pollution—pollution that comes from wide agricultural areas rather than a single point. By pinpointing high-intensity hotspots like potato and vegetable fields, the report offers authorities a framework to improve groundwater management and protect Malta’s long-term water sustainability before the stored pollutants complete their slow journey to the water table.

To help protect the water, the authors recommend labelling greenhouse and vegetable farms as “high-intensity hotspots” in risk models. Experts suggest splitting fertilizer applications into smaller doses to prevent rain from wasting nutrients.

Finally, the team advocates studying how climate variability pushes stored pollutants into the water supply to improve long-term groundwater management and sustainability.

The study did not assess the impact of animal husbandry, which is considered one of the main sources of nitrates in Malta.