Migratory species use multiple habitats types and ecosystems to complete their life cycles, which exposes them to multiple human-caused stressors along their migratory routes. Overexploitation, habitat degradation, invasive species and connectivity loss have contributed to the decrease of migratory fishes globally in particular diadromous fishes that migrate between marine and freshwater systems. Therefore, understanding the joint impacts from anthropogenic disturbances and climate change on different habitats (e.g., both feeding and spawning grounds) and habitat connectivity (e.g., migration routes) is important for conserving migratory fish.Management will be most effective when management scales match ecological scales. This is particularly important for conserving migratory species, because of the requirement of multiple connected habitats that may cross local management boundaries. The main goals of this Ph.D. thesis are to quantify the impacts of multiple stressors on migratory fish species and prioritize management actions for conserving populations (chapters 2 & 3), species (chapter 4), and communities (chapter 5).A central challenge for managing diadromous fishes (species that migrate between freshwater and saltwater ecosystems) is to quantify increases in population persistence from actions that improve connectivity or reduce fishing mortality. In chapter 2, I used a population dynamic model and fish movement data to predict the interactive impacts of fishing pressure and connectivity loss by human modification of river flows on Australian bass Percalates novemaculeata. Then, in chapter 3, the monetary cost of management actions which included seasonal closures and restoring connectivity, were included in the model to find the most cost-effective way to conserve this fish population. The results reveal that the cost-effectiveness of management actions may vary with river flow and fishing pressure before implementing management actions, and implementation times. The spatiotemporal dynamics of how fish species and key resource users (i.e., anglers) respond to management actions can influence the effectiveness of management strategies. Flexible management plans and increased cooperation between water and fishery managers can be used to achieve the most effective balance between conserving migratory fish populations and minimising cost.Migratory species are particularly vulnerable to climate change as they occupy different ecosystems, as well as transitional habitat which are all impacted by climate change differently.Anthropogenic barriers can further reduce the ability of species to respond to a shifting climate. In ii chapter 4, I assessed the impact of climate change on the distribution of a migratory fish species, Australian grayling Prototroctes maraena, and how it affected priorities for restoring connectivity. I found climate change moves at different rates in marine and freshwater systems, decoupling the habitats used by grayling. In addition, the changing spatial distribution of suitable ...