Connectivity in ecological systems is a broad concept that embodies the transmission of ecosystem components throughout landscapes at multiple spatial and temporal scales. Of relevance to the present study are the connections (or lack thereof) among local populations of stream fauna - population connectivity in lotic systems. Dispersal, recolonisation and migration are the demographic forms of population connectivity, and gene flow is the genetic aspect of population connectivity. Both forms of population connectivity have underpinned some of the classic theories and hypotheses in stream ecology, and have implications for pure and applied stream ecology, including ecosystem restoration. Conceptual models in ecology can facilitate understanding and predictability of the ecosystem processes they represent, and have potential applicability as management tools or 'rules of thumb' in conservation and restoration programs. Various theoretical models describe potential patterns of connectivity among local populations and in this thesis these models were used to evaluate population connectivity in a freshwater fish (southern pygmy perch, Nannoperca australis) and two reproductively isolated genetic lineages of freshwater shrimp (Paratya spp.) in small, geomorphically degraded streams in south eastern Australia. These streams (the Granite Creeks) have been the focus of a recent habitat restoration trial and several studies have examined fish and macroinvertebrate community responses to the experiment. It was the purpose of this study to contribute information about population connectivity in the selected species to complement these community ecology studies. Population connectivity was examined in these species using molecular data (mitochondrial and nuclear genetic data) and natural abundance isotopic signatures of nitrogen and carbon. At the landscape scale, results showed that populations of N. australis and the P. australiensis lineages were isolated among the streams and among sites within streams, and that there was no consistent pattern of isolation-by-distance in genetic data for any species. Thus, classic models of population connectivity, such as the Island Model and Stepping-Stone Model, were not supported by this study. Results indicated that population models that incorporated more complex aspects of stream structure may be more appropriate than these classic models for approximating observed patterns of population connectivity in lotic systems. The Stream Hierarchy Model (SHM) predicts that the hierarchical aspect of stream structure (i.e. stream confluences) have a dominant role in shaping patterns of population connectivity in lotic fauna, whereby populations among streams are more isolated than those within them. Although stream confluences were found to have an important role in population subdivision for the species examined in this study, the expectations of the SHM were met for only N. australis. For the P. australiensis lineages, the influence of topography (i.e. the longitudinal aspect of stream structure) was just as important as stream confluences in isolating local populations. Large-scale determinants of population isolation were thus found to be associated with both the hierarchical and longitudinal aspects of stream structure, and were not well represented by any single theoretical model of population connectivity. At within-stream scales, upland populations tended to be extremely isolated from other populations and had temporally stable genetic signatures. In contrast, lowland populations were connected to other lowland populations within the same stream to a greater degree, although the connections were patchy and a slight signature of temporal instability in the genetic data was evident for one of the P. australiensis lineages. Thus, metapopulation or patchy population models were found to represent connections among lowland populations within the same stream, although they were not appropriate for describing connectivity among upland populations. This finding highlights the importance of the longitudinal aspect of stream structure in shaping ecological patterns in lotic systems, and demonstrates that local patterns of population connectivity can vary over relatively small spatial scales. Overall, the results illustrate that both hierarchical and longitudinal aspects of stream structure can have important roles in isolating populations of stream fauna. They therefore also represent constraints for the ability of aquatic fauna to colonise restored habitat in streams. The corollary of this, however, is that such isolated populations of stream fauna represent appropriate population units at which to target habitat restoration. The hierarchical and longitudinal aspects of stream structure may thus represent 'rules of thumb' or 'landscape filters' that stream restoration ecologists could use to predict likely isolated populations of lotic fauna across the landscape. Such a 'rule of thumb' might be the inclusion of multiple isolated population units in restoration programs, as this strategy is likely to generate the greatest biological response to the restoration at the landscape scale, particularly with respect to intra-specific genetic diversity captured by restoration. At small spatial scales, such as for a single stream or tributary, the longitudinal aspect of stream structure can be an important factor to consider when designing stream habitat restoration programs. In this study, lowland sites were unstable and there were patchy connections among local lowland populations within the same stream, whereas upland populations were isolated at this scale. In contrast, other studies have found that upstream populations of some species can be connected in a patchy fashion in other systems. For such unstable sections of stream, where there are patchy patterns of local population connectivity, the inclusion of multiple restored patches, especially refugial habitat, is likely to produce the greatest biotic response at the patch scale, particularly with respect to demographic responses (such as local colonisation). Multiple restored refugial patches will enable species to persist throughout the stream section during adverse environmental conditions, will allow for variation in local movement patterns and distances between species and between years with contrasting environment conditions (e.g. stream flow), and may harbour different species assemblages and intraspecific genotypes due to stochastic processes (i.e. have functional heterogeneity). The hierarchical and longitudinal aspects of stream structure are thus important determinants of population connectivity at both large and small spatial scales, and have implications for how stream biota will respond to restoration at patch and landscape scales.