Polyphenols are plant-derived compounds with known biological activities and potential health benefits. Over the past decade, there are an increasing number of studies have investigated the application of polyphenols and polyphenol-rich additives in aquaculture as functional feed additives. There are several types of polyphenolic compounds such as flavonoids, phenolic acids, lignans, and stilbenes of widely known beneficial influences on the overall performances and immunity of fish, and thereby improving the health status and production of fish farms. This review discusses the beneficial applications, optimum recommended dose, and potential side effects of these natural compounds on the growth performance, proximate body composition, immune responses, disease resistance, reproductive performance, and fillet quality of different fish species. Also, it points out that the biological functions and mechanisms associated with the polyphenolic compounds involved in the pathways of antioxidant and pro-oxidant activities, as well as the modulation of gene expression and different immune parameters. The output of this review article provided overwhelming evidence to support the claim that natural polyphenols can be considered as relatively safe and viable alternatives to synthetic chemical compounds that not only to improve the fish health status but also to enhance the fish quality, productivity, and food safety while reducing the use of chemicals and antibiotics in the aquatic eco-systems.