Material structure has great impact on mass transport properties, a relationship that needs to be understood on several length scales. Describing and controlling the properties of flow through soft materials are both challenges concerning the industrial use of gel structures. This paper reports on how the porous structure in nanoporous materials affects the water transport through them. We used three different silica gels with large differences in the pore sizes but of equal silica concentration. Particle morphology and gel structure were studied using high-resolution transmission electron microscopy and image analysis to estimate the pore size distribution and intrinsic surface area of each gel. The mass transport was studied using a flow measurement setup and nuclear magnetic resonance diffusometry. The average pore size ranged from approximately 500 nm down to approximately 40 nm. An acknowledged limit for convective flow to occur is in the pore size range between 100 and 200 nm. The results verified the existence of a non-linear relationship between pore size and liquid flow at length scales below 500 nm, experimentally. A factor of 4.3 in flow speed separated the coarser gel from the other two, which presented almost identical flow speed data despite a factor 3 in pore size difference. In the setup, the mass transport in the gel with the largest pores was flow dominated, while the mass transport in the finer gels was diffusion dominated. Besides providing new insights into mass transport as a function of pore sizes, we conclude that three-dimensional analysis of the structures is needed for a comprehensive understanding of the correlation between structure and mass transport properties.