The effect of nanostructure of PLD (Pulsed Laser Deposition)-deposited Pd/WO3 sensing films on room temperature (RT) hydrogen sensing properties of SAW (Surface Acoustic Wave) sensors was studied. WO3 thin films with different morphologies and crystalline structures were obtained for different substrate temperatures and oxygen deposition pressures. Nanoporous films are obtained at high deposition pressures regardless of the substrate temperature. At lower pressures, high temperatures lead to WO3 c-axis nanocolumnar growth, which promotes the diffusion of hydrogen but only once H2 has been dissociated in the nanoporous Pd layer. XRD (X-ray Diffraction) analysis indicates texturing of the WO3 layer not only in the case of columnar growth but for other deposition conditions as well. However, it is only the predominantly c-axis growth that influences film sensing properties. Bilayers consisting of nanoporous Pd layers deposited on top of such WO3 layers lead to good sensing results at RT. RT sensitivities of 0.12–0.13 Hz/ppm to hydrogen are attained for nanoporous bilayer Pd/WO3 films and of 0.1 Hz/ppm for bilayer films with a nanocolumnar WO3 structure. SAW sensors based on such layers compare favorably with WO3-based hydrogen detectors, which use other sensing methods, and with SAW sensors with dense Pd/WO3 bilayers.