Hydrothermal environments—where chemical interactions between heated water and rock take place—are of great interest for astrobiology as they may create habitable environments and preserve signs of life. Several planetary bodies display evidence of hydrothermalism, including Mars, which has possessed various hydrothermal environments that could alter organic signals, complicating assessments of biogenicity and our understanding of the depositional environment and subsequent alteration processes. Organic molecules from Earth-based hydrothermal systems serve as an analogue for what we might find on Mars and are typically made up of complex mixtures of in situ and transported molecules that have been altered by diverse mechanisms. Improving our understanding of the processes that drive the preservation and circulation of organic molecules in Earth-based hydrothermal settings is crucial, as the sources and fates of these molecules in marine hydrothermal environments are different from those in subaerial (land-based) hydrothermal environments, even if many of the processes that govern the transport and alteration of this organic matter seem to be similar. To understand the origin of organic molecules found in samples from another world, we must critically evaluate the processes that alter these molecules in terrestrial hydrothermal samples.