Studying the fate of organic carbon in soils and sediments is challenging due mainly to the multiplicity of relationships that exist not only between microbial consortia but between the organic components, nutrients and break down products. Understanding what is happening to carbon in microbial systems would provide valuable information for climate change studies, agricultural planning, pollution studies and more. In this project, a method was developed using gas chromatography-mass spectroscopy (GCMS), isotope ratio mass spectroscopy (IRMS) and nuclear magnetic resonance (NMR) to track 13C in soil biomass. Phospholipid fatty acids (PLFA‘s) identified using GCMS were used as biomarkers to characterise microbial populations, IRMS data revealed which microbial groups were utilizing 13C labelled substrates. NMR allowed the transformations and fate of the carbon substrates to be determined. As the project progressed and developed the techniques were applied to studying organic pollutants and resident microbes in petroleum polluted sites. The method was also transferred to marine sediments, where it was used to study anthropogenic influence on sea bed organic matter in Dublin Bay. Diversifying the application of these methods has allowed us to investigate the fate organic carbon in a variety of scenarios. In incubated soils amended with CO2, glucose and acetate, microbial populations varied with carbon input. Studying carbon sequestration in agricultural soil using these techniques proved that sequestration increased significantly with addition of elemental sulphur. In sites polluted with petroleum compounds GCMS was used to qualify and quantify organic pollutants and characterise the microbial populations present. The study of marine sediment in Dublin Bay revealed significant levels of faecal biomarkers throughout the area and also measurable levels of poly-aromatic hydrocarbons (PAH‘s). The methodology has proven to be adaptable to study carbon compounds in a wide variety of sample types.