Productivity in aquaculture activities is often reduced due to disease outbreaks caused by various pathogens, including bacteria, viruses, and parasites. As an alternative to chemical treatments, a natural, plant-based approach—particularly through the utilization of flavonoid compounds derived from medicinal herbs—is being developed as a safer and more sustainable solution. This paper presents the author’s perspective, based on previous research, on the advantages of using plant-derived flavonoids for the treatment of cultured fish and discusses the potential negative impacts that may arise if such compounds are not integrated into aquaculture systems.