High saturation pools of chlorinated dense non-aqueous phase liquid (DNAPL) are long-term sources of groundwater contamination at many hazardous-waste sites. Recent experiments with DNAPL pools in heterogeneous porous media demonstrated that mass transfer of tetrachloroethene (PCE) can be enhanced significantly by microbe-mediated reductive dehalogenation. Selected mass-transfer experiments have been modeled using MODFLOW/RT3D with a reaction package that includes kinetic mass transfer based on a Gilland-Sherwood expression, and dechlorination of PCE and trichloroethene (TCE) based on Monod kinetics. Traditionally, DNAPL pools have been represented as high saturation zones with minimal advective transport and sharp changes in saturation at pool boundaries. However, efforts to simulate bio-enhanced mass transfer experiments with this concept did not significantly enhance mass transfer. Simulated mixing of electron donor and PCE was limited, and degradationproduct concentrations and mass-transfer rates were less than observed. Detailed mapping of pool morphology identified thin transition zones at the top of pools where DNAPL saturation increased with depth. Reactive-transport modeling based on this description of pool morphology successfully simulated experimental results and showed that hydrodynamics of pool transition zones need to be considered when modeling bio-enhanced mass transfer from DNAPL pools. Advective transport of electron donor within pool transition zones promotes rapid PCE degradation which decreases aqueous-phase PCE concentrations, increases dissolution gradients and enhances mass transfer. At field scales, source-zone characterization of DNAPL represents a difficult challenge. By clarifying the key role of pool morphology in bio-enhanced mass transfer, this study highlights the importance of meeting the challenge.