Local communities are influenced by the fluxes of species across the landscape. Understanding of local patterns of species composition and trophic structure can be enhanced by adopting a metacommunity approach, which combines community dynamics and spatial ecology. Metacommunity studies to date have focused mainly on how dispersal and connectivity affect the diversity of communities, rather than on food web structure. In this study we tested hypotheses about the effects of dispersal limitation, habitat connectivity and ecosystem size on the diversity and food web structure of freshwater metacommunities in Central Australia. Freshwater systems in the arid zone present an opportunity to investigate metacommunity processes on large-scale natural systems with strong barriers to dispersal. We sampled 10 freshwater sites across the West McDonnell and George Gill ranges in the Northern Territory in January 2012 for aquatic invertebrates, water quality and habitat characteristics. Food webs were assembled using literature information and stable isotope analysis. There was no effect of habitat size on food web complexity or on species richness. The communities have similar food web structure and habitat connectivity (to other source communities) was not found to influence food web structure, in spite of the differences in species composition among the communities. This work aim to contribute to a greater understanding of how spatial processes interact to maintain diversity and to generate structure in communities.