Cycling of organic carbon in marine sediments is of fundamental importance for marine ecosystem function, for marine and atmospheric chemistry, for the petroleum and natural gas industry, and for paleoclimatic and paleoenvironmental studies. While most of this carbon is derived from marine and terrestrial sources, significant improvements in mapping and remote investigation have revealed that seabed fluid flow, principally in the form of thermogenic or microbial methane, is also of fundamental importance. In this thesis, the cycling of organic carbon at a number of sites in Irish waters was conducted, with a focus on recently mapped seabed seepage features. A spatial study of the distribution of lipid biomarkers in surface sediments and water column plankton in the western Irish Sea revealed zonation in diatom, zooplankton and dinoflagellate biomass and detrital input in line with hydrographic zonation and seasonal primary production (Chapter 2). Active gas seepage was recorded from carbonate mounds at the Codling Fault Zone, western Irish Sea as well as extensive eroded nodules, largely covered hard ground pavements, patches of anoxic seabed and extensive fossil tube worms and colonising hydroids. Analysis of retrieved samples has confirmed that these hard grounds are methane-derived authogenic carbonates and that anaerobic oxidation of methane is likely a significant process at this site (Chapter 3). The microbial diversity at a large composite but apparently dormant pockmark in the Malin Sea, NW Ireland was found to be dominated by non-seepage associated microbes and suggests a shift in population structure over a pockmarks lifetime. Bacterial species diversity was low and dominated by Psychrobacter and Sulfitobacter genera, although downcore microdiversity is apparent and could indicate niche specialisation with depth (Chapter 4). A shallow pockmark field in Dunmanus Bay was found to coincide with regions of acoustic gas signatures in the upper 3 m of seabed. This has been confirmed to be gas, which most likely accumulated below fine-grained impermeable muddy sediment. Numerous lines of evidence suggest that gaseous products, including methane, are produced in situ rather than transported from the subsurface, suggesting that the role of microbial activity in pockmark formation in this setting could be underestimated(Chapter 5).