Global biodiversity is currently experiencing the sixth major crisis and is declining at an unprecedented rate due to global change and anthropogenic activities. Furthermore, freshwater ecosystems are among the most vulnerable ecosystems, and freshwater fish, as the main biological components of such ecosystems, are increasingly threatened. Accurately assessing the responses of fish populations and communities to environmental changes (e.g., climate change, habitat degradation, biological invasion, and overfishing) and understanding the effect of changes in fish community structure and function on ecosystem functioning are essential to conserving freshwater fish and ecosystems. Recent studies of the functional ecology of freshwater fish have provided a framework for addressing these challenges. Here, we review the methodology, progress, and application of these studies, highlight the functional traits and responses of freshwater fish to environmental changes, discuss the application of new information to fish diversity conservation and fish resource utilization, and propose future research directions.