Water diffusion through natural fibers represents an important aspect with regard to the integrity of biocomposites. Usually, diffusion model is defined assuming circular fiber cross-sections, while microscopic analysis findings revealed other geometries. This was found to affect the modeling of water transport through fibers and provide a gap versus experimental data. This work aims to present a numerical approach using finite element method to overcome the limits of use of analytical approaches relating to the morphological shape of vegetal fibers. The cross-section of the Diss fibers was observed by an optical microscope and simulated at an ellipsoidal shape after processing the images. Then, the average morphological parameters were determined. A numerical finite element model was implemented based on the observed geometry in order to determine the diffusion coefficient by an inverse approach compared to experimental results. The results showed that the numerical approach made it possible to raise the effect of fiber morphology, often assumed to be circular for plant fibers in analytical approaches, on the diffusion coefficient value, which was defined by a unique diffusion coefficient.