Per- and polyfluoroalkyl substances (PFAS) are found throughout the environment due to their chemical stability. Their widespread use in industrial and consumer products has resulted in their frequent detection in aquatic environments, making them contaminants of significant concern. Recent studies focus on the adverse effects of PFAS on aquatic organisms in an effort to elucidate their toxic mechanisms and physiological changes. Here, we comprehensively review the major effects of PFAS on aquatic organisms, including general toxicity, metabolic disruption, and microbiome alterations, and explore how these changes affect biological function and ecosystem balance. In addition to toxic responses in aquatic organisms reported previously, PFAS disrupt metabolic pathways, causing abnormalities in carbohydrate metabolism, lipid homeostasis, and hormonal regulation. They also cause gut microbiome imbalances and reduce the prevalence of beneficial bacteria while promoting pathogen proliferation, which contributes to physiological dysfunction and damages liver and other organ tissues. Experimental evidence emphasizes the multifaceted threats PFAS pose to aquatic health and ecosystem stability and provide a crucial foundation for understanding their long-term impacts from both physiological and ecological perspectives.