Carbon capture and storage (CCS) is a developing technology that seeks to mitigate against the impact of increasing anthropogenic carbon dioxide (CO 2 ) production by capturing CO 2 from large point source emitters. After capture the CO 2 is compressed and transported to a reservoir where it is stored for geological time scales. Potential leakages from CCS projects, where stored CO 2 migrates through the overlaying sediments, are likely to have severe implications on benthic and marine ecosystems. Nonetheless, prokaryotic response to elevated CO 2 concentrations has been suggested as one of the first detectable warnings if a CO 2 leakage should occur. Applying properties of prokaryotic communities (i.e. community composition and metabolic status) as a novel CO 2 monitoring application is highly reliable within a multidisciplinary framework, where deviations from the baseline can easily be identified. In this paper we review current knowledge about the impact of CO 2 leakages on marine sediments from a multidisciplinary-based monitoring perspective. We focus on aspects from the fields of biology, geophysics, and chemistry, and discuss a case study example. We argue the importance of an integrative multidisciplinary approach, incorporating biogeochemistry, geophysics, microbial ecology and modelling, with a particular emphasis on metagenomic techniques and novel bioinformatics, for future CCS monitoring. Within this framework, we consider that an effective CCS monitoring programme will ensure that large-scale leakages with potentially devastating effects for the overlaying ecosystem are avoided. Furthermore, the multidisciplinary approach suggested here for CCS monitoring is generic, and can be adapted to other systems of interest.