We present a lab-on-chip approach to the study of multiphase transport in porous media. The applicability of microfluidics to biological and chemical analysis has motivated much development in lab-on-chip methodologies. Several of these methodologies are also well suited to the study of transport in porous media. We demonstrate the application of rapid prototyping of microfluidic networks with approximately 5000 channels, controllable wettability, and fluorescence-based analysis to the study of multiphase transport phenomena in porous media. The method is applied to measure the influence of wettability relative to network regularity, and to differentiate initial percolation patterns from active flow paths. Transport phenomena in porous media are of critical importance to many fields and particularly in many energy-related applications including liquid water transport in fuel cells, oil recovery, and CO(2) sequestration.