By means of the Non-Smooth Contact Dynamics method allowing modelling the dynamics of granular materials coupled with the Lattice Boltzmann Method to model the fluid dynamic resolved at the sub-particle scale, we numerically simulate the settling of highly polydisperse particles in a viscous fluid. We investigate for this study the effect of the particles size ratio on the structuring of the granular bed after the deposition by analysing: bed porosity, force distribution and contact anisotropy. While the porosity shows to be poorly affected by the polydispersity of particles, a clear size segregation is observed with large particles occupying the bottom part of the deposited granular bed while smaller particles are mainly at the top. This segregation is a direct consequence of the balance between the hydrodynamic forces and the weight of the particles. The contact force shows to be transmitted through large particles.