Landscape connectivity is important for the long-term persistence of species inhabiting dryland freshwater ecosystems, with spatiotemporal surface-water dynamics (e.g., flooding) maintaining connectivity by both creating temporary habitats and providing transient opportunities for dispersal. Improving our understanding of how landscape connectivity varies with respect to surface-water dynamics and land use is an important step to maintaining biodiversity in dynamic dryland environments. Using a newly available validated Landsat TM and ETM+ surface-water time series, we modelled landscape connectivity between dynamic surface-water habitats within Australia’s 1 million km2 semiarid Murray Darling Basin across a 25-yr period (1987–2011). We identified key habitats that serve as well-connected “hubs,” or “stepping-stones” that allow long-distance movements through surface-water habitat networks. We compared distributions of these habitats for short- and long-distance dispersal species during dry, average, and wet seasons, and across land-use types. The distribution of stepping-stones and hubs varied both spatially and temporally, with temporal changes driven by drought and flooding dynamics. Conservation areas and natural environments contained higher than expected proportions of both stepping-stones and hubs throughout the time series; however, highly modified agricultural landscapes increased in importance during wet seasons. Irrigated landscapes contained particularly high proportions of well-connected hubs for long-distance dispersers, but remained relatively disconnected for less vagile organisms. The habitats identified by our study may serve as ideal high-priority targets for land-use specific management aimed at maintaining or improving dispersal between surface-water habitats, potentially providing benefits to biodiversity beyond the immediate site scale. Our results also highlight the importance of accounting for the influence of spatial and temporal surface-water dynamics when studying landscape connectivity within highly variable dryland environments.