We study here the interplay between transport and adsorption in porous systems with complex geometries under a fluid flow. Using a Lattice Boltzmann scheme extended to take into account adsorption at solid/fluid interfaces, we investigate the influence of pore geometry and internal surface roughness on the efficiency of fluid flow and the adsorption of molecular species inside the pore space. We show how the occurrence of roughness on pore walls acts effectively as a modification of the solid/fluid boundary conditions, introducing slippage at the interface. We then compare three common pore geometries, namely honeycomb pores, inverse opal, and materials produced by spinodal decomposition. Finally, we quantify the influence of those three geometries on fluid transport and tracer adsorption. This opens perspectives for the optimization of materials geometries for applications in dynamic adsorption under fluid flow.