Disruption of movement patterns is a pervasive effect of humans on animal populations. In many terrestrial and aquatic circumstances there is increasingly tension between the need to simultaneously allow passage of some species while blocking the passage of other species. We explore the ecological basis for developing selective passage methods with a focus on riverine fishes, where the need to restrict movements of invasive species conflicts with the need to allow passage of species of commercial, recreational, or conservation concern. We develop a trait-based framework for selective fish passage based on understanding of the types of movements displayed by fishes and the role of filters in determining the spatial distributions of fishes. We then synthesize information on trait-based mechanisms to create a multi-dimensional niche space based on attributes such as physical capabilities, body morphology, sensory capabilities, behavior, and movement phenology. Following this, we review how these mechanisms have been applied to achieve selective fish passage. To date, trap-and-sort or capture-translocation efforts provide the best options for movement filters that are completely species selective, but these methods are hampered by the continual and high cost of manual sorting. Other less effective methods of selective passage risk collateral damage in the form of lower or higher than desired levels of passage. Fruitful areas for future work include using combinations of ecological and behavioral traits to passively segregate species; using taxon-specific chemical cues in a push-pull arrangement to direct unwanted species away from passageways and into physical or ecological traps; and developing automated sorting mechanisms based on fish recognition systems. The trait-based approach proposed for fishes could serve as a template for selective passage in other ecological circumstances.