The geographically isolated, environmentally unique and biologically diverse coral reefs of north-west Australia are under threat from climate change and other localised human impacts. Similar to many other regions around the world, effective mitigation of these threats through ecosystem-based marine spatial planning is currently constrained by a lack of knowledge of the extent and direction of dispersal of eggs, larvae, recruits, juveniles or adults among the coral reefs (termed population connectivity). Here, we present the outcomes of a series of consultations between Marine Protected Area planners, managers and scientists aimed at facilitating the integration of this connectivity knowledge into effective management guidelines and policy in north-west Australia. Through this process, we first synthesised current knowledge of population connectivity in the fields of oceanography, larval biology and population genetics, and then identified and answered to the best of our ability the most useful questions for the spatial planning of Marine Protected Area networks. Key findings indicate that these systems are likely ecologically independent for many coral reef organisms, with hard corals exhibiting the most localised dispersal of species studied so far. Thus, given that hard corals are also the habitat forming species, and that more widely dispersing species such as fish are likely less vulnerable to small scale disturbance, we propose that no-take areas that facilitate resilience of hard coral populations should maximise biodiversity more generally. This means no-take areas that are large enough to encompass routine dispersal distances of corals (10–20 km), and are spaced at similar distances, will not only maintain self-replenishment, but also aid recovery after disturbance through connectivity between no-take areas. The results can be applied in a regional and wider context, and provide a valuable template for transfer of scientific knowledge into effective policy.