Seepage-induced instabilities pose a challenge in many geotechnical applications. Particle-scale mechanisms govern the initiation of instability. However, current understanding is based on a macro-scale perspective that draws on continuum mechanics. Recent developments in imaging and numerical analysis can provide the particle-scale fundamental perspective needed to develop a comprehensive insight. This contribution demonstrates the value of combining particle-scale experimental and numerical studies. The experiments consider transparent soil samples created using refractive image matching and monitored by particle image velocimetry (PIV). Three-dimensional pore topology is extracted from a series of two-dimensional images and imported into computational fluid dynamics (CFD) simulations. Permeability is estimated by three distinct approaches: using flow rate, PIV- and CFD-generated data. The flow fields obtained from PIV and CFD are in good agreement considering both flow rate contour plots and flow rate distributions; this demonstrates the successful reconstruction of three-dimensional pore structure and flow-field analysis. The comparison also reveals that the side boundary effects in CFD simulations are constrained within a limited region. The multi-plane results characterise the variance of flow velocity with the three-dimensional pore topology. Finally, the fluid–particle interactions obtained from CFD results show a larger variance in the angular particle packings.