Migratory organisms carry high ecological and cultural significance as their cyclic movements through time and space create influxes of nutrients into ecosystems and provide important sources of food to people - imprinting on cultures, bodies of practice and management as well as knowledge systems. However, their often long-distance movements between habitats expose them to multiple and potentially interacting risks. Migratory Pacific salmon (Oncorhynchus spp.) are threatened by a suite of stressors, both known (e.g., overfishing, climate change) and unknown, that jeopardize their wellbeing as well as that of linked social-ecological systems. A central focus of this thesis is to elucidate the ultimate fate (i.e., survival to spawning grounds) of salmon who encounter fishing gears but either escape or are released as bycatch, and how this fate is shaped by other factors at play (such as rising temperatures). To gain an improved understanding of what other potential factors may be, a second focus here is to identify leading threats endangering salmon and aquatic ecosystems more generally. Different ways of knowing are valued and interwoven in this work, motivated by the Mi'kmaw conceptual framework of Etuaptmumk or "Two-Eyed Seeing" which creates a pathway for learning from both Indigenous and Western sciences, using their distinct strengths and methodologies in tandem. Experimental fisheries approaches, carried out in partnership with local and Indigenous fishers and fisheries managers, reveal that the context of salmon capture influences upstream survival, with the severity of the capture experience, the damage incurred to fish in the process and surrounding environmental conditions (such as water temperature) each being predictive of fate. Two expert threat assessments involving international freshwater scientists and Indigenous knowledge holders, respectively, identified multiple shared concerns (e.g., climate change, infectious diseases, habitat loss, hydroelectric projects) and numerous place-based stressors of local significance for wild salmon populations. Each assessment revealed a profound change in the state of freshwater biodiversity and Pacific salmon harvests over time, respectively, with both declining by an average of 83% between ~1970 and present - signaling the urgency of conservation actions that protect fresh waters, their inhabitants and all that they underpin for people and place.