<p dir="ltr">In a rapidly changing world, human actions and natural events are reshaping ecosystems and presenting new challenges for conservation efforts. Within this context, unraveling the recent ecosystem transformations and their implications on a fine scale is required. The impacts of such changes are not always sudden but often gradual and sometimes as a result of historical events. With the recent advancement in technologies, the resolution of information by genome sequences spans from millions of years ago (hindcasting) to future generations (forecasting). Aquatic ecosystems pose their own challenges when it comes to ecosystem changes and the types of data required to assess impact and help inform conservation efforts. My dissertation comprises three chapters focused on using genomic techniques to generate data valuable for the conservation and management of aquatic ecosystems. Each of the three chapters is a distinct manuscript in terms of scientific publications, where Chapter 1 has already been published, Chapter 2 has been submitted to a journal, revised, and is now awaiting publication, and Chapter 3 is in preparation for submission to a peer-reviewed journal. In Chapter 1, dietary DNA from harvested North American river otter (<i>Lontra canadensis</i>)<i> </i>was used to determine whether metabarcoding of stomach content could be used to identify fish prey species consumed. In Chapter 2, DNA sequencing of endangered pupfish species in the Tularosa Basin of New Mexico was studied; before my work, it was nominally comprised of a single species, the White Sands pupfish (<i>Cyprinodon tularosa</i>). The results indicate a rapid speciation event occurred within about the last ~5000 years, driven primarily by genetic drift. Chapter 3 extends Chapter 2 by assessing the dynamics of genomic diversity over space and time while evaluating the short-term evolutionary dynamics (~18 generations) of the two native pupfish populations. This temporal study aimed to determine if the extraordinarily rapid evolution over the last ~5000 years (observed in Chapter 2) could be detected over timescales more relevant to conservation and management efforts. Overall, this dissertation used genomic sequence data from metabarcoding of the COI gene region in the otter stomach content as well as pool sequencing and whole genome resequencing of pupfish to provide key biological insights into the conservation of these aquatic species. This dissertation also provides insights into avenues for further study and highlights the significant role that conservation genomics can play in the future. The findings presented in the three chapters are discussed within the context of species’ conservation and management.</p>