<p>Cyanobacteria, among the most ancient and versatile microorganisms on Earth, thrive across different aquatic ecosystems, ranging from freshwater to marine environments. In addition to being important producers of structurally diverse secondary metabolites, these photosynthetic prokaryotes are crucial to the global cycling of carbon and nitrogen. With their wide range of biological activities, such as antibacterial, antiviral, anticancer, and anti-inflammatory properties, cyanobacterial metabolites are attractive options for use in biotechnology and medicine. In addition, some cyanometabolites have toxic properties that affect aquatic ecosystems and present problems for human health and water quality. This dual significance for ecology and biomedicine emphasizes how crucial it is to do systematic research on cyanobacterial metabolites. The chemical diversity, biological roles, and biosynthetic origins of cyanobacterial secondary metabolites are summarized in this review, with a focus on their translational potential and ecological responsibilities. Innovative approaches for accelerating metabolite discovery and characterization are also covered, including recent developments in metabolite profiling, genome mining, and artificial intelligence (AI)-assisted biosynthetic gene cluster prediction. The present review integrate ecological, biochemical, and computational perspectives emphasizes the cyanobacteria is ongoing significance as sources of bioactive chemicals for environmental sustainability, pharmaceutical research, and biotechnology.</p>