Understanding the coupling between rock permeability, pore pressure, and fluid flow is crucial, as fluids play an important role in the Earth’s crustal dynamics. We measured the distribution of fluid pressure during fluid-flow experiments on two typical crustal lithologies, granite and basalt. Our results demonstrate that the pore-pressure distribution transitions from a linear to a non-linear profile as the imposed pore-pressure gradient is increased (from 2.5 MPa to 60 MPa) across the specimen. This non-linearity results from the effective pressure dependence of permeability, for which two analytical formulations were considered: an empirical exponential and a new micromechanics-based model. In both cases, the non-linearity of pore pressure distribution is well predicted. However, using a compilation of permeability vs. effective pressure data for granites and basalts, we show that our micromechanics-based model, which combines the rough crack asperity model and cubic law theories, outperforms the exponential formulation at low effective pressures.