To study the change of chromium speciation in the Cr(VI) natural attenuation processes, which involve both the diffusion and redox reaction of Cr(VI), Cr(VI) diffusion-reaction experiments for carbonate rock samples were conducted. The synchrotron radiation μ-XRF and SEM-EDS mapping revealed that in organic-rich carbonate rock samples, fresh precipitated Cr was mainly located near the surface and associated with organic matters. Whereas, in the sample with low organic matter, Cr was distributed evenly. These results indicate that the organic matter in the fractures and pore space is the major natural reductant that reacts with Cr(VI) in organic-rich samples, and forms reducing products (Cr(III) precipitates), which might aggregate and block the pore throats, and prevent further diffusion of Cr(VI) into the rock matrix. The synchrotron radiation X-ray absorption near-edge structure (XANES) was used to obtain the distributions of Cr chemical forms. The results show that for organic-rich 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 carbonate rock samples, the Cr(III) hydroxides, which aggregate in the zones near 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 process. This work provides a feasible way to investigate the change of chromium chemical speciation during its diffusion-reaction processes in rock samples using synchrotron radiation techniques.