The effectiveness of low salinity flooding for enhanced oil recovery (EOR) in sandstone reservoirs has been demonstrated in core plug and field tests as well as at molecular scale, but in carbonate reservoirs the results are mixed. With atomic force microscopy (AFM) chemical force mapping (CFM), using a methyl (CH3) functionalized tip, we tracked the wettability of limestone pore surfaces (before and after solvent treatment) during exposure to high and low salinity solutions at a submicrometer scale. The correlation between adhesion and salinity was weak for both the treated and the fresh samples, but detailed analysis of the force maps demonstrated that on the fresh limestone there are areas that clearly respond to changes in salinity. Adhesion decreased when salinity decreased on some areas, and on others adhesion increased. To understand this behavior, we analyzed the surfaces with X-ray photoelectron spectroscopy (XPS) and energy dispersive X-ray spectroscopy (EDXS). The amount of organic material on the solvent treated samples was lower than on the fresh samples, but the amount and type of organic compounds were considerably different. These differences provide a likely explanation for the differences in the effectiveness of low salinity flooding that have been reported in the literature and lead us to conclude that for the samples analyzed in our study, the response in carbonate rocks is controlled by an intricate interplay between the composition of the tightly adsorbed organic material, the minerals on which it is adsorbed, and the functional groups present in the oil. Consequently, if the effectiveness of low salinity flooding in carbonate reservoirs is to be predicted, characterization of the organic compounds in the oil and on the pore surfaces is essential.