This Special Issue of 12 full-length papers collectively addressed biotic scales from (i) salmonid skin microbiomes to (ii) cyprinid genetics and ecology to (iii) assessment of ichthyoplankton and older fishes across freshwater and estuarine habitats. The focus was typically guild- or assemblage-oriented to better assess anthropogenic impacts, but it also included a single-species study that examined geographic variation in catfish ecology in the face of climate crisis pressures. The genetic, microbiologic, habitat, trophic, and hydrologic ecology of fishes that were discussed should help us to better assess anthropogenic impacts in other contexts. We hope this Special Issue provides a springboard for other aquatic ecologists to formulate more holistic, ecosystem-health assessments, especially by spatiotemporal planning, to minimize impacts to rare and migratory species.