This paper synthesizes recent works at the interface of hydrology, geomorphology, and ecology under an integrated framework of analysis with an aim for a general theory. It addresses a wide range of related topics, including biodiversity of freshwater fish in river networks and vegetation along riparian systems, how river networks affected historic spreading of human populations, and how they influence the spreading of water-borne diseases. Given the commonalities among various dendritic structures and despite the variety and complexity of the ecosystems involved, we present here an integrated line of research addressing the above and related topics through a unique, coherent ecohydrological thread and similar mathematical methods. Metacommunity and individual-based models are studied in the context of hydrochory, population, and species migrations and the spreading of infections of water-borne diseases along the ecological corridors of river basins. A general theory emerges on the effects of dendritic geometries on the ecological processes and dynamics operating on river basins that will establish a new significant scientific branch. Insights provided by such a theory will lend themselves to issues of great practical importance such as integration of riparian systems into large-scale resource management, spatial strategies to minimize loss of freshwater biodiversity, and effective prevention campaigns against water-borne diseases.