Resistance to fluid flow within cartilage extracellular matrix is provided primarily by a dense network of rod-like glycosaminoglycans (GAGs). If the geometrical organization of this network is random, the hydraulic permeability tensor of cartilage is expected to be isotropic. However, experimental data have suggested that hydraulic permeability may become anisotropic when the matrix is mechanically compressed, contributing to cartilage biomechanical functions such as lubrication. We hypothesized that this may be due to preferred GAG rod orientations and directionally-dependent reduction of inter-GAG spacings which reflect molecular responses to tissue deformations. To examine this hypothesis, we developed a model for effects of compression which allows the GAG rod network to deform consistently with tissue-scale deformations but while still respecting limitations imposed by molecular structure. This network deformation model was combined with a perturbation analysis of a classical analytical model for hydraulic permeability based on molecular structure. Finite element analyses were undertaken to ensure that this approach exhibited results similar to those emerging from more exact calculations. Model predictions for effects of uniaxial confined compression on the hydraulic permeability tensor were consistent with previous experimental results. Permeability decreased more rapidly in the direction perpendicular to compression than in the parallel direction, for matrix solid volume fractions associated with fluid transport in articular cartilage. GAG network deformations may therefore introduce anisotropy to the permeability (and other GAG-associated matrix properties) as physiological compression is applied, and play an important role in cartilage lubrication and other biomechanical functions.