Organic geochemistry is the study of the sources, transport, and fate of carbon based molecules in the environment. In particular, lipid biomarkers are employed as a means of tracking this carbon and understanding the complex interactions involved in its global biogeochemical cycling. In this thesis, organic geochemical techniques were applied to several research areas to glean information from organic matter in an effort to answer several research questions. In Chapter 2, lipid biomarkers derived from faecal material were analysed from archaeological soils in the Italian Alps. This data provided potential evidence of the passage of Hannibal of Carthage’s army as it crossed the Alps to invade Italia in 218 BC. Analysis of material from a peat bog in Spiddal, Co. Galway which featured the remnants of a ‘drowned forest’ provided a record of Ireland’s palaeoclimate during the Mid-Holocene in Chapter 3. Evidence of significant climatic events were uncovered including a cool period in the Northern Hemisphere attributed to the ‘4.2 ka event’. A warming climate and rising sea levels ca. 2000 BP were suggested as possible factors in the drowning of the forest. In Chapter 4, a characterisation of gas seepage in Bantry Bay, Co. Cork was carried out. Sites included an area of seabed depressions known as a pockmark field. Geophysical and geochemical data suggested that these seafloor features were formed via the expulsion of biogenic methane from deep within the sediments of the bay. Porewater geochemistry and lipid biomarker analysis revealed distinct sulphate methane transition zones (SMTZ) beneath the seafloor and provided an insight into the microbial activity of the area including the occurrence of the anaerobic oxidation of methane (AOM).