X-ray micro-tomography combined with a high-pressure high-temperature flow apparatus and advanced image analysis techniques were used to image and study fluid distribution, wetting states and oil recovery during low salinity waterflooding (LSW) in a complex carbonate rock at subsurface conditions. The sample, aged with crude oil, was flooded with low salinity brine with a series of increasing flow rates, eventually recovering 85% of the oil initially in place in the resolved porosity. The pore and throat occupancy analysis revealed a change in fluid distribution in the pore space for different injection rates. Low salinity brine initially invaded large pores, consistent with displacement in an oil-wet rock. However, as more brine was injected, a redistribution of fluids was observed; smaller pores and throats were invaded by brine and the displaced oil moved into larger pore elements. Furthermore, in situ contact angles and curvatures of oil–brine interfaces were measured to characterize wettability changes within the pore space and calculate capillary pressure. Contact angles, mean curvatures and capillary pressures all showed a shift from weakly oil-wet towards a mixed-wet state as more pore volumes of low salinity brine were injected into the sample. Overall, this study establishes a methodology to characterize and quantify wettability changes at the pore scale which appears to be the dominant mechanism for oil recovery by LSW.