Hydrophobic organic compounds (HOCs) represent a class of generally highly persistent contaminants in groundwater. Factors influencing the transport of HOCs are evaluated through a hierarchical modeling approach, which incorporates particle scale sorption/diffusion with pore scale flow and transport models. The relative contributions of transport- and sorption-related factors on HOCs transport are first elucidated in a simplified single particle system. The comparative roles of different soil organic matter contents and compositions on the fate and transport of HOCs are further investigated by simulation of phenanthrene transport in porous media. This effort represents a proof-of-concept demonstration of bridging comprehensive representations of fluid-flow with mechanistic sorption/desorption processes.