Over the past decade, hydraulic fracturing combined with horizontal drilling has become the dominant technique for extracting shale gas in the US, and is increasingly important globally. A complex mixture of chemicals is used in hydraulic fracturing fluid to stimulate natural gas production, but federal regulations have exempted operators from reporting the specific chemicals used in any given well. Recent state-by-state regulations and voluntary disclosures have increased our understanding of these fluids, but knowing this list of chemicals going into a well is just the tip of the iceberg. Once these chemicals are injected, they mix with fluids and naturally occurring chemicals originating in the shale formation and can undergo physical, chemical, and biological transformations. In Chapter 2, I reviewed the literature to date regarding the characterization of organic compounds in injected hydraulic fracturing fluids and waste fluids returning to the surface. I identified a substantial knowledge gap in our understanding of organic compounds in these fluids, particularly non-volatile compounds, and potential transformations within the organic compound pool over the lifetime of the well. I analyzed a number of different shale gas wastewaters using ultrahigh resolution mass spectrometry and identified halogenated organic compounds in these fluids (Ch. 3), suggesting that these compounds were transformation products. Using a time series of shale gas fluids (Ch. 4), I was able to track changes in halogenated organic compounds and find evidence for both biological and chemical transformation pathways. Hierarchical cluster analyses helped identify sulfur-containing transformation products (Ch. 4), and I then determined that sulfur-containing molecules may be useful tracers of shale gas wastewaters in the environment (Ch. 6). In Chapter 5, I used toxicological tests and photoirradiation experiments to track the fate of organic compounds in shale gas wastewaters. Using a primarily non-targeted approach, I have been able to identify a number of organic compounds that are indicative of biological and chemical transformations occurring within hydraulic fracturing fluids and wastewaters. Understanding how these fluids change within the well and during storage and disposal provides critical information for engineering the safe and effective operation of wells, wastewater treatment techniques, and environmental impacts.