Abstract Fractures are ubiquitous on all scales in crustal rocks. The investigation of fractures and their influence on physical and transport properties of rocks is therefore essential for understanding of many key problems in seismology, volcanology and rock engineering. In crystalline rocks, pore water is primarily stored in and migrates through networks of cracks and fractures at all scales. It is therefore essential to know how fluid flow in such fracture networks responds to the elevated pressures found at depth. Here, we report results from an investigation of changes in fluid permeability, and associated changes in P-wave and S-wave velocities, at elevated effective pressure for intact, macro-fractured and micro-fractured samples of Seljadur basalt. In all cases, permeability decreases and both wave velocities increase with increasing effective pressure. Permeability decreases were smallest in the intact material (from approximately 10 −19 m 2 to 3 × 10 −20 m 2), intermediate in the micro-fractured material (from approximately 5 × 10 −17 m 2 to 1 × 10 −17 m 2) and largest in the macro-fractured material (from approximately 3 × 10 −15 m 2 to 9 × 10 −19 m 2). For a material containing both micro-fractures and macro-fractures, the closure of macro-fractures dominated the permeability reduction at low pressure, with the closure of micro-fractures exerting an increasing influence at higher pressure.