Interbasin water transfer projects, in which river connectivity is restructured via man-made canals, are an increasingly popular solution to address the spatial mismatch between supply and demand of fresh water. However, the ecological consequences of such restructuring remain largely unexplored, and there are no general theoretical guidelines from which to derive these expectations. River systems provide excellent opportunities to explore how network connectivity shapes habitat occupancy, community dynamics, and biogeographic patterns. We apply a neutral model (which assumes competitive equivalence among species within a stochastic framework) to an empirically derived river network to explore how proposed changes in network connectivity may impact patterns of freshwater fish biodiversity. Without predicting the responses of individual extant species, we find the addition of canals connecting hydrologically isolated river basins facilitates the spread of common species and increases average local species richness without changing the total species richness of the system. These impacts are sensitive to the parameters controlling the spatial scale of fish dispersal, with increased dispersal affording more opportunities for biotic restructuring at the community and landscape scales. Connections between isolated basins have a much larger effect on local species richness than those connecting reaches within a river basin, even when those within-basin reaches are far apart. As a result, interbasin canal projects have the potential for long-term impacts to continental-scale riverine communities.