This work was conducted to study the risk of formation damage as the result of mineral scales deposition during smart waterflooding into carbonate core sample, as well as the influence of injected water salinity and ionic composition on mineral scaling and precipitation. The reservoir flowing conditions were simulated by a new laboratory core-flooding procedure, which took into count of the effect of in-situ contact time (CT) of injected water and formation water on scaling. After the optimum CT was determined, extent of permeability decline was studied by the change in the salinity and ionic composition of injection seawater. The scaled core sample was analyzed visually by scanning electron microscopy (SEM) to study the crystal morphology of the scale. Under the experimental conditions, extent of permeability decline caused by CaSO4 and CaSO3 composite scales ranged from 61% to 79.1% of the initial permeability. The salinity and the ionic composition of injected smart water, and CT of the mixing waters had significant effects on the co-precipitation of CaSO4 and CaSO3 scales. The SEM images reveal that the loss of permeability is mainly caused by the accumulation and growth perpendicular to the pore wall of scale crystals.