Cumulative effects from multiple anthropogenic stressors over the past three centuries have severely impacted estuarine and coastal habitats, with cascading effects on the species that rely upon them. Pacific salmon (Oncorhynchus sp.) are migratory species that use estuaries as juveniles and as adults and deliver critical nutrients to coastal ecosystems as they move between fresh and marine waters. Many once abundant salmon populations have been extirpated or are in severe decline relative to historic levels, yet the strength of the relationship between habitat loss and population productivity has been challenged. In this dissertation, I applied field studies, otolith analyses, and conservation decision science tools to investigate the relative importance of estuarine habitat to salmon populations, with the aim of advancing effective management solutions for these species and their habitats. First, I conducted a two-year field survey of fish communities in the Fraser River estuary, British Columbia, Canada comparing the species richness and relative catch amongst three distinct habitats. I found that this impacted estuary still supported a rich community of migratory marine and anadromous fishes, as well as resident estuarine fish species. Each habitat supported some unique fish assemblages, with eelgrass supporting the highest catch and diversity of fishes overall but brackish marsh supporting the highest and most consistent catch of salmonids. Next, I used otolith analyses to quantify the residency and growth of juvenile Chinook salmon in the estuary. I found that for one of the only two remaining Chinook salmon stocks abundant enough to still support limited harvest in the Fraser River, the estuary provides vital rearing habitat, with juveniles residing in the estuary for an average of 6 weeks, during which time they had mean daily growth rates of 0.57 mm fork length, approximating growth in healthier estuarine systems. The use of these habitats by juvenile Chinook salmon had not been quantified previously, so these findings directly inform management of this population, which was recently designated as Threatened by the Committee on the Status of Endangered Wildlife in Canada. Finally, I applied Priority Threat Management, a conservation decision science framework, to predict the future status of Pacific salmon in the lower Fraser River and identify the most cost-effective conservation solutions out of a suite of alternative management strategies. On our current trajectory none of these populations were predicted to be assessed as ‘green’ or healthy status at the end of 25 years. In contrast, implementation of broad scale habitat restoration, protection, and watershed management could considerably improve the viability of the lower Fraser to support these salmon, such that many (14/19) of these populations would have a >50% likelihood of being assessed as healthy. Together, this research provides novel evidence of active and selective use of estuarine habitats by juvenile salmon, reliance on estuarine habitat for early marine growth by juvenile Chinook salmon, and a direct link between habitat health and population status for lower Fraser River salmon populations. / Graduate / 2023-04-13