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The primary objective of this thesis was to combine a chemical degradation technique together with an analytical framework centered primarily around gas chromatography (GC) to more fully interrogate the composition of aquatic dissolved organic matter (DOM). Previous studies had suggested that aliphatic compounds could represent a significant fraction of refractory organic matter isolated by solid phase extraction (SPE). These studies had also uncovered the vast complexity of DOM. Gas chromatography coupled to mass spectrometry provides superior separation capability and is ideal for examining complex mixtures of lipid-derived molecules. As such I sought to develop a comprehensive GC analysis methods to provide molecular level information for DOM isolated by solid phase extraction (SPE) onto a hydrophobic resin- PPL (Agilent Bond Elut). In Chapter II, a comprehensive chemical reduction procedure was developed and first applied to the environmental DOM standard Suwannee River Fulvic Acid (SRFA) as a proxy for marine DOM. The resulting hydrocarbons were amenable to comprehensive gas chromatography time-of-flight mass spectrometry (GCxGC-TOF-MS), and effectively resolved into multiple series of alicyclic, unsaturated compounds. This was the first direct demonstration of the isomeric complexity of aquatic DOM. Similar alicyclic compounds were recovered from the reduction of terrestrial source material, implicating resin acids and sterols as potential precursors of SRFA. In Chapter III the reduction process was applied to marine surface DOM from the Scripps Institution of Oceanography Pier, and similar alicylic compounds were found. The GCxGC-TOF-MS identified carbon backbones closely resembling carotenoids, implicating these ubiquitous and highly reactive biomolecules as the source of a significant fraction of DOM accumulating in the marine water column. The structural assignment was supported by the identification of carotenoid derived resonances in two dimensional nuclear magnetic resonance (NMR) spectra, which indicated that these molecules were highly oxidized compared to the parent molecules consistent with their present in DOM. Following up on this work in Chapter IV the carotenoid β-carotene was irradiated with natural sunlight to test the hypothesis that photodegradation was one pathway that converted carotenoids into water-soluble degradation products. The first finding was that the reaction produced a series of compounds identical to compounds isolated from marine DOM. The second important result was that the reaction produced a complex mixture of isomers from a single compound that helps to at least partly explain the compositional diversity in marine DOM. Together, the data in Chapters III and IV allowed us to link a large fraction of DOM to a ubiquitous biomolecule that can now serve as a model for studies examining the formation and fate of DOM that accumulates in the ocean on long timescales. Finally, in Chapter V we sought to examine how the composition of DOM – both the complex alicyclic fraction and small, polar biomolecules, which are considered a “fresher” signal of biological input – evolved across a salinity gradient. Although core biochemical classes were present in all regions the data supported in situ production of compositionally similar material rather than mixing across the gradients as proposed in some studies. Together, the chapters in my thesis provide new insight in the composition of dissolved organic matter in marine and terrestrial environments. The thesis also represents the most comprehensive molecular level characterization of DOM isolated by this solid phase extraction method, which is the most commonly used isolation method in the field. My findings also provide an important foundation for future lab-based mechanistic studies of DOM cycling in the marine environment.