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The expanding field of nutraceuticals and functional food science is increasingly turning to marine-derived bioactive compounds, particularly saponins, for their diverse pharmacological properties. These so-called thalassochemicals display distinctive structural features—such as sulfated glycosidic moieties and amphiphilic backbones—that underpin potent antitumor, hypolipidemic, antioxidant, and antimicrobial activities. In contrast to their terrestrial analogs, marine saponins remain underexplored, and their complexity poses analytical and functional challenges. This review provides a critical and integrative synthesis of recent advances in the structural elucidation, biological function, and technological application of marine saponins. Special emphasis is placed on the unresolved limitations in their isolation, characterization, and structural validation, including coelution of isomers, adduct formation in MS spectra, and lack of orthogonal techniques such as NMR or FTIR. We illustrate these limitations through original MS/MS data and propose experimental workflows to improve compound purity and identification fidelity. In addition to discussing known structure–activity relationships (SARs) and mechanisms of action, we extend the scope by integrating recent developments in computational modeling, including machine learning, molecular descriptors, and quantitative structure–activity relationship (QSAR) models. These tools offer new avenues for predicting saponin bioactivity, despite current limitations in available high-quality datasets. Furthermore, we include a classification and comparison of steroidal and triterpenoid saponins from marine versus terrestrial sources, complemented by detailed chemical schematics. We also address the impact of processing techniques, delivery systems, and bioavailability enhancements using encapsulation and nanocarriers. Finally, this review contextualizes these findings within the regulatory and sustainability frameworks that shape the future of saponin commercialization. By bridging analytical chemistry, computational biology, and food technology, this work establishes a roadmap for the targeted development of marine saponins as next-generation nutraceuticals and functional food ingredients. Full article