To study the Cr(VI) natural attenuation processes, Cr(VI) diffusion-reaction experiments for limestone samples were conducted. After experiments, synchrotron radiation µ-XRF maps showed that for organic-rich limestone samples, most of Cr distributed close to the surface, and some high Cr spots were found to be associated with organic matters; whereas, Cr distributed evenly in the samples containing low organic matter. These results indicate that Cr(VI) reacts with organic matter in the fractures and pore space of organic-rich limestone samples, and the reducing products (Cr(III) precipitates) might aggregate and block the pore throats, which might retard the further diffusion of Cr(VI) into the rock matrix. The distributions of Cr chemical forms, which were obtained by X-ray absorption near-edge structure (XANES) spectroscopy, showed that for organic-rich limestone samples, the Cr(OH)3 fraction in the center was higher than that on the surface, whereas, for the samples containing low organic matter, no such significant difference was found. One possible explanation for these findings is that in organic-rich limestone samples, the Cr(III) hydroxides, which aggregate in the zones close to the surface, might age and transform from crystalline to the stable chemical forms of Cr(III) oxyhydroxide or even Cr(III) oxides, which could enhance the effect of Cr(VI) natural attenuation. By using synchrotron radiation based techniques, this work provides a feasible way to investigate the changes of chromium chemical forms during its diffusion-reaction processes in rock samples and can be used to study the mechanism of Cr(VI) natural attenuation.