Freshwater ecosystems and their associated biota are among the most endangered in the world. Key threats to these ecosystems include dams and water withdrawals that alter natural flow regimes, modifications of riparian and in-stream habitats, invasive species, and impacts on water quality from sediment, nutrients, and toxic pollutants. Direct habitat alteration and destruction of freshwater ecosystems have resulted from agriculture practices and urban expansion. Subsistence, recreational and commercial fisheries place further stresses on declining species and can alter ecosystem function. Escalating human pressure on, and disturbances to, water resources requires well-informed decision making and effective on-ground management to conserve and restore freshwater ecosystems. Systematic conservation planning offers the tools needed to address these issues, providing a strategic and scientifically defensible framework. However, in comparison to the terrestrial and marine realms, the adoption of systematic methods to inform decision making for the protection and/or restoration of freshwater ecosystems remains in its infancy. In my thesis I addressed the following gaps in systematic conservation planning literature: 1) representation of freshwater ecosystems and dependent species represented under regional terrestrial protected area networks, and the prominent threats impinging upon these systems and species; 2) effectiveness of coarse-filter surrogates (e.g., habitat types) for representing freshwater fish species in conservation planning exercises; 3) effectiveness of invasive species management actions at reducing invasive species abundance; and 4) cost-effectiveness of systematic approaches compared to ad hoc approaches used to prioritise invasive species management. My thesis has not only contributed to the advancement of the theory of systematic conservation planning, my work has also demonstrated the applicability of this framework for solving real-world conservation resource allocation problems.