This study evaluates the technical, design, and economic feasibility of large-scale hydrogen storage in deep water-bearing geological formations (aquifers), presenting it as a scalable solution for seasonal energy storage within the European Union’s decarbonization framework. A techno-economic model was developed for a 1 BCM facility, integrating geomechanical, microbial, and thermodynamic criteria. The results indicate a recoverable hydrogen fraction of 70–85%, with dissolution and microbial conversion losses limited to below 10% under optimized operational regimes. Geochemical and microbiological modelling demonstrated that sulfate-reducing and methanogenic bacterial activity can be reduced by 80–90% through controlled salinity and pH management. The proposed design, incorporating high-permeability sandstone reservoirs (100–300 mD), hydrogen-resistant materials, and fibre-optic monitoring ensures stable containment at 60–100 bar pressure and enables multi-cycle operation with minimal leakage (<0.05% per year). Economically, the baseline Levelized Cost of Hydrogen Storage (LCOHS) for aquifers was found to be ~0.29 EUR/kWh, with potential reductions to ~0.18 EUR/kWh through optimized drilling, modularized compression systems, and microbial mitigation. The lifecycle carbon footprint (0.20–0.36 kg CO2-eq/kg H2) is competitive with other geological storage methods, while offering superior scalability and strategic flexibility.