Declining aquatic biodiversity is a primary threat to ecosystem and human health globally. Basic biological information is necessary to conserve biodiversity, but even that information is missing for as many as ~30% of freshwater species. Evolutionary biology methods can rapidly fill in knowledge gaps and enhance conservation efforts for understudied species, provided they are combined with robust sampling design and ecological data collection. Using whole genome sequencing and modeling approaches, researchers can identify species boundaries, population structure, intraspecific genetic diversity, and threats to extinction based on recent evolutionary history. This dissertation addresses knowledge gaps for two declining aquatic species using genomic data, field observations, and population modeling. I first assessed the species status of the Summer Sucker (Catostomus utawana), an extreme life history variant of the White Sucker (C. commersonii), which spawns at small size and later in the spring season. In my second chapter, I describe the genomic mechanisms underlying evolution of the Summer Sucker in two lakes, testing for evidence of selection, and the role of genomic architecture and certain genes in each lake. In my third chapter, I combined findings from these studies to inform modeling of hypothetical evolutionary scenarios that could have favored the emergence of the Summer Sucker phenotype. I found that the phenotypic and genomic features of Summer Suckers are convergently evolved, and that the recent evolutionary history of Summer Sucker populations supports revision of its taxonomy from species to ecotype. Life history modeling using integral projection models identified key traits and ecological processes that may have driven within-lake divergence between Summer Sucker and White Sucker populations. My fourth chapter used genomic data to describe population structure, genomic variation, and local adaptation in a commercially important marine invertebrate in Alaska, the red king crab (Paralithodes camtschaticus). I uncovered new genetic groupings and evidence of local adaptation that support geographically localized management of red king crab populations. Taken as a whole, my dissertation adds management-relevant information to the literature on two declining species in freshwater and marine environments. In each case, this information will be used by regional managers to conserve intraspecific diversity that is important to the long term survival of each species. Beyond these two study systems, my findings show that the genetic mechanisms driving intraspecific diversity are themselves diverse, and that a broader knowledge of evolution in non-model organisms is necessary to understand how eco-evolutionary dynamics drive biodiversity among aquatic animals.