Mixing controls the fate of any solute entering porous media. Hence, an understanding of the involved processes is essential for assessing subsurface contamination and planning for its protection. However, the three‐dimensional mechanisms dominating solute mixing in the presence of several fluid phases in the pore space, and their dependency on phase saturation degree (fraction of the pore volume occupied by a phase) are unknown. Here, we analyze solute mixing in unsaturated porous media at the pore scale using X‐ray micro‐tomography performed with synchrotron radiation at unprecedented temporal and spatial resolutions for such an investigation. Transport experiments through a synthetic, sand‐like porous medium, followed in 4D using a contrast solution, are performed at different liquid phase saturation degrees. The results reveal larger solute's front deformation at lower saturation, which translates into an enhanced mixing with time. Using different topological indexes, defined based on a description of the liquid phase geometry and of the resulting hydrodynamics, we show an increase in the spatial convergence of flow streamlines at lower saturation, which, in turn, leads to a strengthened helical flow inside the liquid phase. Consequently, this increases the number of shear‐ and vorticity‐dominated deformation regions, as characterized by larger negative and positive Q‐criterion values, respectively. These findings represent a major step toward understanding the control of both saturation and the system's heterogeneity on solute mixing, essential, among others, to assess reactivity in porous media.