We present in this study results from X-ray tomographic microscopy with synchrotron radiation performed both in attenuation and phase contrast modes on a limestone sample during two stages of water drying. No contrast agent was used in order to increase the X-ray attenuation by water. We show that only by using the phase contrast mode it is possible to achieve enough water content change resolution to investigate the drying process at the pore-scale. We performed 3D image analysis of the time-differential phase contrast tomogram. We show by the results of such analysis that it is possible to obtain a reliable characterization of the spatial redistribution of water in the resolved pore system in agreement with what expected from the theory of drying in porous media and from measurements performed with other approaches. We thus show the potential of X-ray phase contrast imaging for pore-scale investigations of reactive water transport processes which cannot be imaged by adding a contrast agent for exploiting the standard attenuation contrast imaging mode. X-ray tomographic imaging is an ideal method for investigating at the pore scale and in 3D liquid transport processes in porous materials because it allows nowadays achieving very high temporal and spatial resolutions, especially when synchrotron radiation is used. In the last years, an increasing number of pore-scale studies have exploited such method to improve our understanding of such diverse phenomena as displacement of oil by water in rocks, transport of contaminants through soils, transport of liquids in engineering porous materials affecting their durability and lifetime. Since water weakly attenuates X-rays and the standard approach in X-ray imaging exploits X-ray photon photoelectric absorption, the degree of attenuation by the liquid is typically enhanced by “doping” it with tracer particles or by dissolving a salt, all made of high density or high atomic number elements. Such approach, based upon “contrast agents” has been exploited in biomedical Xray imaging since very long time and has been very successful. Contrast agents imply a lot of drawbacks when the liquid transport process is reactive, i.e., when the liquid chemically interacts with the host porous material. In many cases, e.g., water transport in cement-based materials or liquefied CO2 transport in rocks, it is necessary not to perturb the couplings between the chemical reactions and the liquid transport because they are key investigation targets for the process to be studied, e.g., understanding how water affects the microstructure evolution during cement hardening and the stability/potentiality of CO2 storage in a given type of geologic site. Thus one may not be able to use contrast agents, in order not to change the chemical reactions. We show in this work that X-ray tomographic microscopy based upon phase, instead of attenuation, contrast retains the high temporal/spatial resolution while achieving sufficient contrast to resolve distilled water content changes at the pore scale, without the need of any contrast agent. Our work is focused in this case on visualizing and characterizing, by 3D image analysis, the spatial temporal distribution patterns of water in a natural limestone subject to evaporative drying. However, the imaging and image analysis approaches proposed in this article have a broader impact for 3D imaging of reactive water (or other liquid) transport processes in both natural and engineered porous materials.