Understanding the interplay between local conditions, species traits and spatial factors is critical foundation knowledge for effective management of biodiversity. We sampled aquatic communities in three chain-of-pools stream systems in central Victoria over three years. We sampled at the scale of the pool, the reach and the sub-catchment. We assessed a range of local habitat factors at each scale, and calculated simple Euclidean, stream network and resistance-weighted stream network measures of connectivity between all pools. Species were attributed dispersal traits from existing databases. Community composition was strongly structured by spatial factors in interaction with dispersal traits. A set of common taxa were present at all scales and were characterised by good dispersal ability and/or factors that made them resistant to reduced flows. Other taxa showed evidence of being dispersal limited, with a strong spatial signature in their occurrence. Local conditions were important for a small group of taxa, particularly shredders, but the communities were generally characterised by habitat and trophic generalists. These results show the importance of a whole-of-network perspective in managing local conditions for biodiversity.