Agriculture, the largest global water consumer, accounts for ~70% of freshwater use thereby considerably influencing water availability. The use of treated wastewater [TWW] for agricultural irrigation has been suggested as a possible solution to help mitigate water scarcity without disrupting food production. However, despite the benefits of TWW irrigation, it is often characterized by high salinity that can reduce crop performance and damage soil structure. In Israel, over 50% of the water used for irrigation is TWW, and a third of the produced TWW undergoes soil aquifer treatment [SAT], i.e., infiltration and percolation to groundwater through the soil before utilization for irrigation. In parallel, seawater desalination provides about 80% of the urban and industrial sector water use. These developments in Israel's water economy during the last three decades, accompanied by extensive governmental monitoring, enabled us to harness high-resolution nation-wide datasets to study the effects of the large-scale introduction of desalination and SAT on TWW quality and salinity in particular. The analyses revealed that large-scale desalination considerably reduced the salinity of TWW to levels similar to freshwater (up to 70% and 60% for Cl and Na, respectively). However, sodium absorption ratio remained unchanged due to the concurrent reductions of Na, Ca and Mg. Mg was reduced to levels that can potentially harm both crops and human health, while B concentrations increased to levels of possible toxicity to crops, suggesting the need for stringent requirements in the post-treatment process. Salinity of groundwater was increased by SAT in the long-term, but was reduced after the introduction of desalination. The results, encompassing almost three decades of water monitoring, suggest that high-quality TWW with a significant portion of desalinated base-water can provide groundwater salinity remediation services.