Understanding the flow dynamics of hydrogen-water in aquifers is critical to maximizing hydrogen storage and recovery. By using direct computational fluid dynamics at elevated pressure, this paper aims at detailed pore-scale investigation of the effect of flow regime, compressibility, and hysteresis on flow pattern, trapping mechanisms and the efficiency of hydrogen storage and recovery. The results reveal that the favorable rates during hydrogen injection and production differ and a medium flow rate corresponding to drainage capillary number of ∼10−7 and imbibition capillary number of ∼10−5 can minimize both capillary and viscous fingering mechanisms, leading to more storability and recovery factor. We show that neglecting the local compression and expansion of hydrogen and a low working pressure, typical in modeling and experimental studies, result in misinterpretation of flow regimes and hydrogen storability. Finally, we report that during the cyclic process, the trapped hydrogen bubbles produce a “self-cushion gas" effect, improving hydrogen storage.