The structural and dynamic properties of fluids under confinement in a porous medium differ from their bulk properties. This study delves into the surface structuring and hydrodynamic characteristics of oil/thin film carbonated brine two-phase within a calcite channel upon salinity variation. To this end, both equilibrium and non-equilibrium molecular dynamics simulations are utilized to unveil the effect of the carboxylic acid component (benzoic acid) in a simple model oil (decane) confined between two thin films of carbonated brine on the oil–brine–calcite characteristics. The salinity effect was scrutinized under four saline carbonated waters, deionized carbonated water (DCW), carbonated low-salinity brine (CLSB, 30,000 ppm), carbonated seawater (CSW, 60,000 ppm), and carbonated high-salinity brine (CHSB, 180,000 ppm). An electrical double layer (EDL) is observed at varying salinities, comprising a Stern-like positive layer (formed by Na+ ions) followed by a negative one (formed by Cl– ions primarily residing on top of the adsorbed sodium cations). By lowering the salinity, the Na+ ions cover the interface regions (brine–calcite and brine–oil), depleting within the brine bulk region. The lowest positive surface charge on the rock surface was found in salinity corresponding to seawater. Two distinct Na+ peaks at the oleic phase interface have been observed in the carbonated high-salinity brine system, enhancing the adsorption of polar molecules at the thin brine film interfaces. There is a pronounced EDL formation at the oleic phase interface in the case of CSW, resulting in a strong interface region containing ions and functional fractions. Likewise, the oil region confined by CSW exhibited the lowest apparent viscosity, attributed to the optimized salinity distribution and inclination of benzoic acid fractions uniformly at the brine–oil interface, acting as a slippery surface. Moreover, the results reveal that the presence of polar fractions could increase the oil phase’s apparent viscosity, and introducing ions to this system reduces the polar molecules’ destructive effect on the apparent viscosity of the oil region. Therefore, the fluidity of confined systems is modulated by both composition of the brine and oil phases.