Biological communities often occur in spatially structured habitats where connectivity directly affects dispersal and metacommunity processes. Recent theoretical work suggests that dispersal constrained by the connectivity of specific habitat structures, such as dendrites like river networks, can explain observed features of biodiversity, but direct evidence is still lacking. We experimentally show that connectivity per se shapes diversity patterns in microcosm metacommunities at different levels. Local dispersal in isotropic lattice landscapes homogenizes local species richness and leads to pronounced spatial persistence. On the contrary, dispersal along dendritic landscapes leads to higher variability in local diversity and among-community composition. Although headwaters exhibit relatively lower species richness, they are crucial for the maintenance of regional biodiversity. Our results establish that spatially constrained dendritic connectivity is a key factor for community composition and population persistence.