Diatoms are a major group of microalgae found in marine and freshwater environments. They are widely recognized for their role in primary production and global carbon cycling and silica deposition. Currently, they have gained attention for their remarkable capacity to produce a wide array of secondary metabolites. These bioactive compounds are known to serve various ecological functions, such as deterring grazers, mediating interspecies interactions, and shaping the microbial communities, thereby influencing the structure and dynamics of aquatic ecosystems. The ecological role of these metabolites also helps to modulate nutrient cycles, support symbiotic associations, and increase the survival of diatom populations under environmental stress. Recent developments in omics technologies, particularly functional genomics and metabolomics, have greatly elevated our understanding of the metabolic pathways and regulatory networks responsible for production of metabolites in diatoms. These insights have opened new pathways for exploring the potential applications of diatom-derived compounds in pharmaceuticals, nutraceuticals, and environmental remediation. Despite this progress, challenges remain due to the few numbers of fully sequenced diatom genomes and the complexity of metabolite profiling under variable environmental conditions. In future, multidisciplinary approaches combining taxonomy, synthetic biology, bioinformatics, and artificial intelligence are expected to advance the discovery and application of diatom metabolites. However, ethical and regulatory framework, ecological risks associated with bioprospecting, and large-scale exploitation must be taken into consideration. This chapter underlines the immense unexplored potential of diatom secondary metabolites and highlights the need for continued research to utilize them for ecological and industrial purposes responsibly.