The existing system of nature reserves in Australia is inadequate for the long-term conservation and restoration of native biological diversity because it fails to accommodate, among other elements, large scale and long-term ecological processes and change, including physical and biotic transport in the landscape. This paper is an overview of the connectivity elements that inform a scientific framework for significantly improving the prospects for the long-term conservation of Australia's biodiversity. The framework forms the basis for the WildCountry programme. This programme has identified connectivity at landscape, regional and continental scales as a critical component of an effective conservation system. Seven categories of ecological phenomena are reviewed that require landscape permeability and that must be considered when planning for the maintenance of biological diversity and ecological resilience in Australia: (1) trophic relations at regional scales; (2) animal migration, dispersal, and other large scale movements of individuals and propagules; (3) fire and other forms of disturbance at regional scales; (4) climate variability in space and time and human forced rapid climate change; (5) hydroecological relations and flows at all scales; (6) coastal zone fluxes of organisms, matter, and energy; and, (7) spatially-dependent evolutionary processes at all scales. Finally, we mention eight cross-cutting themes that further illuminate the interactions and implications of the seven connectivity-related phenomena for conservation assessment, planning, research, and management, and we suggest how the results might be applied by analysts, planners, scientists, and community conservationists.