Intensive irrigated agriculture substantially modifies the hydrological cycle and often has major environmental impacts. The article focuses upon a specific concern—the tendency for progressive long-term increases in the salinity of groundwater recharge derived from irrigated permeable soils and replenishment of unconfined aquifers in more arid regions. This process has received only scant attention in the water-resource literature and has not been considered by agricultural science. This work makes an original contribution by analysing, from scientific principles, how the salinisation of groundwater recharge arises and identifies the factors affecting its severity. If not proactively managed, the process eventually will impact irrigation waterwell salinity, the productivity of agriculture itself, and can even lead to land abandonment. The types of management measure required for mitigation are discussed through three detailed case histories of areas with high-value groundwater-irrigated agriculture (in Spain, Argentina and Pakistan), which provide a long-term perspective on the evolution of the problem over various decades.