Large-scale underground hydrogen storage (UHS) in carbonate saline aquifers is a promising method to address the challenges of the clean energy transition. This type of UHS uses the pores of carbonate rock layers deep below the surface to store hydrogen at high pressure. However, injecting hydrogen in these systems can lead to activity and growth of microorganisms that metabolize hydrogen, and to geochemical reactions with the groundwater and minerals present. This is important because it can cause hydrogen loss, fouling and blockage of the hydrogen flow in and out of the UHS. Currently, a thorough understanding of the complex system dynamics of these interactions is missing. This project will address this gap by examining the interplay between hydrogen reactivity and flow processes in carbonate saline aquifers at the µm- to cm-scale, using a case-study of a potential UHS site in Belgium. A multidisciplinary approach will be used, combining geoscience and microbial ecology to study model systems with gradually increasing complexity: static batch experiments, microfluidic chips, and fractured rock samples. The study will explain the fundamental mechanisms governing these UHS and their implications on larger scales, facilitating informed decision-making, reservoir selection, and sustainable implementation of large-scale hydrogen storage technologies.