Reverse osmosis (RO) has been increasingly applied for impaired water reuse in arid areas. However, enhancing RO recovery from scarce water resources is limited by energy demand for overcoming elevated brine osmotic pressure, and membrane scaling caused by concentrated poorly soluble salts. In this study, we present a hybrid ion exchange desalination process (HIX-Desal) as multifunctional RO pretreatment to enhance RO recovery by simultaneously desalinating feed water and removing multiple scale-forming ions (calcium, sulfate, and phosphate). The novelty of HIX-Desal is that carbon dioxide was the sole regenerant for a two-column train containing a hybrid anion exchanger (HAIX, with doped ferric oxide nanoparticles) and a shallow shell weak acid cation exchanger (SSWAC). We probed the desalination abilities of HIX-Desal at both lab and pilot scales using impaired water sources with varying total dissolved solids (TDS), where consistent desalination was achieved at 50–60% TDS reduction. Field tests demonstrated >80% removal of calcium, sulfate, and phosphate simultaneously. System configuration and SSWAC structure, i.e., intraparticle diffusion path length, were demonstrated to govern the HIX-Desal process during desalination and CO2 regeneration cycle. We envision this study to facilitate RO recovery enhancement and upcycling industrial carbon emission. •Multifunctional RO pretreatment was achieved using ion exchange driven by CO2.•50% TDS reduction was achieved using impaired water in both lab and field tests.•Phosphate, sulfate, and calcium were simultaneously removed using two-column system.•Column sequence and resin structure were key for desalination and CO2 regeneration.