- Abstract The processes affecting salinization of precipitation, surface water, vadose water and groundwater were studied in the Negev desert, Israel. Observations spanning 18 years included the collection of rainfall at three rain sampling stations, flood water at six flood stations, vadose water from four coreholes penetrating chalk formations, and groundwater from 16 monitoring wells tapping the chalk aquitard. Dissolved carbonate dust and evaporation of the falling raindrops result in Ca(HCO 3 ) 2 facies and increased ion concentration of the rainwater with respect to inland, more humid regions. The exposure of flood water to evaporation during flood events is minimal. The observed Ca(HCO 3 ) 2 facies and salt enrichment by a factor of three to five in the flood water with respect to precipitation results primarily from interactions of the flood water with the chalk and limestone bedrock, including ion exchange on Na- and K-bearing minerals and the dissolution of calcite, gypsum and halite. The presence of these salts at and near land surface results from the complete evaporation of rainwater in land surface depression storage areas following most rain events. Except for a small portion moving through the low permeability chalk matrix, most of the vadose water moves through preferential pathways and is typically not exposed to evaporation. This dual movement of water accounts for the NaCl facies of vadose water and the variable rates of isotopic depletion and salt dilution observed in the underlying heterogeneous groundwater in the saturated zone. Although the variable mixing with low-salinity, isotopically depleted water percolating from the fractures accounts for the depleted isotopic composition of the groundwater, its relatively low solute content cannot modify the groundwater NaCl facies. Consequently, only groundwater salinity in the chalk is reduced by the preferentially flowing water, but the Ca(HCO 3 ) 2 facies prevailing in the rainwater and flood water disappears, and the NaCl imprint from the vadose zone prevails.