The effect of flow regime and fluid morphology (distribution and spatial arrangement) on macroscopic transport properties (effective diffusion coefficient, hydraulic conductivity) was analyzed using a multi-component lattice Boltzmann model. Various flow regimes for two-phase flow in porous media have been defined: stable displacement, capillary fingering, and viscous fingering. The dominance of one regime over another in a porous medium of interest is controlled by the relative magnitudes of gravity, viscous, and capillary forces, which can be quantified with three parameters: Bond number Bo, capillary number Ca, and their difference, Bo-Ca. It has been shown that macroscopic transport properties in porous media are highly dependent on fluid configuration. Since the three flow regimes exhibit very different fluid morphologies, it seems likely that flow regime will have a significant effect on diffusion and hydraulic conductivity. Accordingly, a series of imbibition simulations in each of the flow regimes was carried out by varying Ca and Bo. Results were compared to experimentally-derived images from the literature. Unsaturated hydraulic conductivity curves and effective diffusion coefficient curves were generated as a function of water saturation for each flow regime and compared to theoretically-determined curves. Significant differences are seen in the curves for the fingering regimes compared to the stable displacement and theoretical curves.