Short-chain fatty acids (SCFAs) are small organic acids exist in the fish gastrointestinal tract, mainly acetate, propionate, and butyrate. These SCFAs are produced through anaerobic fermentation of dietary non-digestible carbohydrates by gut microbes. Though enough studies have been devoted to showcasing the potential of SCFAs in human nutrition, the research on their production, potential, and existence in fish has been comparatively limited until recently. This review aims to provide a comprehensive overview of the current knowledge regarding SCFAs in aquaculture. It starts with commenting on the different sources, such as substrate and microbial species that are responsible for the production of SCFAs and their transportation and ends up depicting the relationship between biofloc technology and SCFAs production. This review also discusses the factors influencing SCFA production, such as environment, diet, and feeding habits of fish. Furthermore, the biological functions of SCFAs have been highlighted, and critical findings were compiled, including immunomodulatory effects, physiological response, gut health, and immunity.