Numerical models that solve transport of pollutants at the macroscopic scale in unsaturated porous media need the effective diffusion dependence on saturation as an input. We conducted numerical computations at the pore scale in order to obtain the effective diffusion curve as a function of saturation for an academic sphere packing porous medium and for a real porous medium where pore structure knowledge was obtained through X-ray tomography. The computations were performed using a combination of lattice Boltzmann models based on two relaxation time (TRT) scheme. The first stage of the calculations consisted in recovering the water spatial distribution into the pore structure for several fixed saturations using a phase separation TRT lattice Boltzmann model. Then, we performed diffusion computation of a non-reactive solute in the connected water structure using a diffusion TRT lattice Boltzmann model. Finally, the effective diffusion for each selected saturation value was estimated through inversion of a macroscopic classical analytical solution