In heap leach operations, metal recovery is fundamentally controlled by the ore's particle size distribution (PSD), which determines mineral exposure characteristics, the rate of leaching reactions, and fluid flow phenomena. A fluent circulation of solution through the heap is important for successful leach plant operation. The pore networks inside 6-in. diameter leach columns from the Rochester mine were scanned by X-ray Computed Tomography (XCT) at a voxel size of 100 μm, to estimate the permeability by Lattice Boltzmann Method (LBM). The bottom sections of 6-in. columns had much less porosity and corresponding permeability than the top sections. PSD of the bottom and top sections showed no migration of fines, and gravity compression reduced the bottom sections' permeability. The pore networks inside 4-in. diameter leach columns with controlled PSD were scanned by XCT at a higher resolution with a voxel size of 68 μm. In addition to the large particles (rocks) and pore network, another phase of agglomerated fines from local fluid movement was identified. This phase of agglomerated fines can overwhelm the volume of the pore network inside leach columns and thus reduce the permeability, leading to possible ponding issues in the heap.