In landscapes where natural habitat is highly fragmented, any method for assessment of population persistence or potential for biodiversity should be based upon metapopulation theory, taking into account the spatial and temporal dynamics of species. We argue that methods based upon species distribution data, population viability analyses (PVA), or landscape indices alone all have severe flaws. We introduce an approach based upon a combination of the three methods, in which ecologically scaled landscape indices (ESLI) are compared to spatial standards derived from both analysis of distribution data and PVA-type simulations. We derive spatial standards, introducing the key patch approach. Key patches are large patches with a stabilizing role in habitat networks. Key patch standards were developed using spatial analysis of presence–absence data and calibrated metapopulation models for marshland bird species. We show examples of the application of this approach in land use management at both regional and national planning scales.