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Worldwide, fishways are increasingly criticized for failing to meet conservation goals. We argue that this is largely due to the dominance of diadromous species of the Northern Hemisphere (e.g., Salmonidae) in the research that underpins the concepts and methods of fishway science and management. With highly diverse life histories, swimming abilities and spatial ecologies, most freshwater fish species do not conform to the stereotype imposed by this framework. This is leading to a global proliferation of fishways that are often unsuitable for native species. The vast majority of fish populations do not undertake extensive migrations between clearly separated critical habitats, yet the movement of individuals and the genetic information they carry is critically important for population viability. We briefly review some of the latest advances in spatial ecological modelling for dendritic networks to better define what it means to achieve effective fish passage at a barrier. Through a combination of critical habitat assessment and the modelling of metapopulations, climate change-driven habitat shifts, and adaptive gene flow, we recommend a conceptual and methodological framework for fishway target-setting and monitoring suitable for a wide range of species. In the process, we raise a number of issues that should contribute to the ongoing debate about fish passage research and the design and monitoring of fishways.