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The transport of particles and fluids through multichannel microfluidic networks is influenced by details of the channels. Because channels have micro-scale textures and macro-scale geometries, this transport can differ from the case of ideally smooth channels. Surfaces of real channels have irregular boundary conditions to which streamlines adapt and with which particle interact. In low-Reynolds number flows, particles may experience inertial forces that result in trans-streamline movement and the reorganization of particle distributions. Such transport is intrinsically 3D and an accurate measurement must capture movement in all directions. To measure the effects of non-ideal surface textures on particle transport through complex networks, we developed an extended field-of-view 3D macroscope for high-resolution tracking across large volumes ($$25\,\hbox {mm} \times 25\,\hbox {mm} \times 2\,\hbox {mm}$$$25\text{mm}\times 25\text{mm}\times 2\text{mm}$) and investigated a model multichannel microfluidic network. A topographical profile of the microfluidic surfaces provided lattice Boltzmann simulations with a detailed feature map to precisely reconstruct the experimental environment. Particle distributions from simulations closely reproduced those observed experimentally and both measurements were sensitive to the effects of surface roughness. Under the conditions studied, inertial focusing organized large particles into an annular distribution that limited their transport throughout the network while small particles were transported uniformly to all regions.