There are critical opportunities and profound challenges at the food-water-energy nexus. Crucial to the global nexus is the role of groundwater. Groundwaters provide 99% of the world’s useable freshwater supplies. Irrigation is required for much of the world’s food production, as 40% of the food grown globally uses irrigation. Yet some 10% of today’s irrigation water is “stolen” from tomorrow, as it relies on today’s use of non-renewable groundwater. With “business-as-usual,” it is predicted we will reach “peak groundwater” around 2050. We review groundwater-protection measures under two contrasting food-production systems: viticulture in temperate New Zealand, and halophyte production for food, fibre, and fuel in the hyper-arid United Arab Emirates (UAE). Some 75% of New Zealand’s wine is produced in the Marlborough region, and the vines generally require irrigation using groundwater. Our in-situ measurements of drainage and leaching show that there is net drainage-recharge of groundwater, and that the nitrate concentrations in the leachates are less than the drinking water standard. Groundwater is being protected though a net aquifer recharge of about 100 mm·a⁻¹. Our work in the UAE focussed on groundwater protection under the production of the obligate halophyte Salicornia using irrigation with the reject brine from a desalination unit. A leaching-fraction is needed to despatch the residual salts out of the rootzone back to groundwater. Our heuristic modeling predicts a hyperbolic rise in aquifer salinity. From an initial salt concentration of 18.8 kg·m⁻³, the concentration of salt would be predicted to reach about 100 kg·m⁻³ in just 40 years. Solutions to extend the life of these groundwaters could involve the use of zero-liquid-discharge desalination, or the conjunctive use of alternative waters, either directly, or indirectly via managed aquifer recharge. There are opportunities and challenges at the nexus. Solutions will rely on engineering science and technology.