We study geochemical processes along the variably‐saturated zone during managed aquifer recharge (MAR) with reverse‐osmosis desalinated seawater (DSW). The DSW, post‐treated at the desalination plant by calcite dissolution (remineralization) to meet the Israeli water quality standards, is recharged into the Israeli Coastal Aquifer through an infiltration pond. Water quality monitoring during two MAR events using suction cups and wells inside the pond indicates that cation exchange is the dominant subsurface reaction, driven by the high Ca2+ concentration in the post‐treated DSW. Stable isotope analysis shows that the shallow groundwater composition is similar to the recharged DSW, except for enrichment of Mg2+, Na+, Ca2+, and . A calibrated variably‐saturated reactive transport model is used to predict the geochemical evolution during 50 years of MAR for two water quality scenarios: (i) post‐treated DSW (current practice) and (ii) soft DSW (lacking the remineralization post‐treatment process). The latter scenario was aimed to test soil‐aquifer‐treatment (SAT) as an alternative post‐treatment technique. Both scenarios provide an enrichment of ∼2.5 mg L−1 in Mg2+ due to cation exchange, compared to practically zero Mg2+ currently found in the Israeli DSW. Simulations of the alternative SAT scenario provide Ca2+ and remineralization due to calcite dissolution at levels that meet the Israeli standard for DSW. The simulated calcite content reduction in the sediments below the infiltration pond after 50 years of MAR was low (<1%). Our findings suggest that remineralization using SAT for DSW is a potentially sustainable practice at MAR sites overlying calcareous sandy aquifers.