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Freshwater ecosystems constitute only a small fraction of the planet's water resources, yet support much of its diversity, with freshwater fish accounting for more species than birds, mammals, amphibians or reptiles. Fresh waters are, however, particularly vulnerable to anthropogenic impacts, including habitat loss, climate and land use change, pollution and biological invasions. This environmental degradation, combined with unprecedented rates of biodiversity change, highlights the importance of robust and replicable programmes to monitor freshwater fish. Such monitoring programmes can have diverse aims, including confirming the presence of a single species (e.g., early detection of alien species), tracking changes in the abundance of threatened species, or documenting long-term temporal changes in entire communities. Irrespective of their motivation, monitoring programmes are only fit for purpose if they have clearly articulated aims and collect data that can meet those aims. This review, therefore, highlights the importance of identifying the key aims in monitoring programmes and outlines the different methods of sampling freshwater fish that can be used to meet these aims. We emphasize that investigators must address issues around sampling design, statistical power, species' detectability, taxonomy and ethics in their monitoring programmes. Additionally, programmes must ensure that high-quality monitoring data are properly curated and deposited in repositories that will endure. Through fostering improved practice in freshwater fish monitoring, this review aims to help programmes improve understanding of the processes that shape the Earth's freshwater ecosystems and help protect these systems in face of rapid environmental change.