Today, decisions regarding the management and conservation of populations are often informed to some degree by population genetics. A fundamental measure sought by decisionmakers is the degree of connectivity between populations, which, when approached from a genetic perspective, may be influenced by many factors, making it difficult to generalize across taxa, habitats, or life histories. In the case of freshwater-limited fauna, the shared constraint of habitat structure (e.g., a dendritic stream network) imposed on all species in the system simplifies the task. A number of models have been proposed that predict how populations of taxa with different life-history traits and dispersal capabilities interact within structured freshwater habitats of this kind. In this article, we summarize these models and illustrate the general patterns of phylogeographic structure expected to occur under different scenarios of freshwater population connectivity. Additionally, we describe how the genetic structure of stream inhabitants can reflect historical changes in the physical structure of streams and thus open a window on past patterns of connectivity. A greater understanding of these concepts will contribute to an improved multidisciplinary approach to managing freshwater ecosystems.