Aim Recent efforts to apply the principles of systematic conservation planning to freshwater ecosystems have focused on the special connected nature of these systems as a way to ensure adequacy (long-term maintenance of biodiversity). Connectivity is important in maintaining biodiversity and key ecological processes in freshwater environments and is of special relevance for conservation planning in these systems. However, freshwater conservation planning has focused on longitudinal connectivity requirements within riverine ecosystems, while other habitats, such as floodplain wetlands or lakes and connections among them, have been overlooked. Here, we address this gap by incorporating a new component of connectivity in addition to the traditional longitudinal measure. Location Northern Australia. Methods We integrate lateral connections between freshwater areas (e.g. lakes and wetlands) that are not directly connected by the river network and the longitudinal upstream–downstream connections. We demonstrate how this can be used to incorporate ecological requirements of some water-dependent taxa that can move across drainage ivides, such as waterbirds. Results When applied together, the different connectivity rules allow the identification of priority areas that contain whole lakes or wetlands, their closest neighbours whenever possible, and the upstream/downstream reaches of rivers that flow into or from them. This would facilitate longitudinal and lateral movements of biota while minimizing the influence of disturbances potentially received from upstream or downstream reaches. Main conclusions This new approach to defining and applying different connectivity rules can help improve the adequacy of freshwater-protected areas by enhancing movements of biodiversity within priority areas. The integration of multiple connectivity needs can also serve as a bridge to integrate freshwater and terrestrial conservation planning.