The modification of hydrophobic rock surfaces to the water-wet state via nanofluid treatment has shown promise in enhancing their geological storage capabilities and the efficiency of carbon dioxide (CO2) and hydrogen (H2) containment. Despite this, the specific influence of silica (SiO2) nanoparticles on the interactions between H2, brine, and rock within basaltic formations remains underexplored. The present study focuses on the effect of SiO2 nanoparticles on the wettability of Saudi Arabian basalt (SAB) under downhole conditions (323 K and pressures ranging from 1 to 20 MPa) by using the tilted plate technique to measure the contact angles between H2/brine and the rock surfaces. The findings reveal that the SAB's hydrophobicity intensifies in the presence of organic acids, with significant increases in both advancing (θa) and receding (θr) contact angles upon exposure to organic acid at 323 K and 20 MPa. Contrastingly, the application of SiO2 nanoparticles under these conditions results in a marked shift towards hydrophilicity, with θa and θr decreasing substantially, thus indicating an optimal nanoparticle concentration (0.1 wt% SiO2) for effecting the transition from H2-wet to water-wet states. This change in wettability aligns with the known pressure-dependent behavior of contact angles. Moreover, the treatment of organically-aged basalt with 0.1 wt% SiO2 nanofluids at 20 MPa and 323 K enhances the H2 column height significantly, from −424 m to 4340 m, suggesting a reduced risk of H2 migration across the caprock and thereby enhancing both the structural/residual trapping and containment security of H2 within the basaltic formations of Saudi Arabia. This article highlights the crucial role of SiO2 nanofluids in improving the efficacy of H2 storage in basalt, offering a new insight towards the optimization of geological storage solutions for hydrogen, a critical component in the transition to a sustainable energy future.