Climate-change-induced freshwater shortage and saline intrusion have been posing significant risks to agricultural sectors in arid and semi-arid regions, negatively impacting irrigation, crop yield, and food production. Climate-smart sustainable solutions are the requirement to combat these major concerns. To overcome freshwater scarcity, pressure-driven desalination techniques are used that require advanced operational systems and electricity, which creates an additional economic burden when applied in the agriculture sector. Therefore, more sustainable methods for soil and water desalination using plant-, microbial-, algal-, biomass-, and carbon-based systems are needed. This scoping review addresses the effects of climate change on freshwater shortage and global food production, the influence of salinity and sodicity on agriculture, and sustainable desalination technologies.