Abstract

Aquatic ecosystems, especially the marine and freshwater habitats, are good sources of bioactive compounds that have great potential in the pharmaceutical industry. These bioactive molecules are alkaloids, terpenoids, carotenoids, sulfated polysaccharides, and peptides, and have a variety of therapeutic effects, including anticancer, antimicrobial, and anti-inflammatory effects. Although this has potential, the extraction procedures, sustainable harvesting, and scaleability of aquatic biodiversity pose challenges to drug discovery. This paper will examine the development of aquatic pharmaceutical biotechnology with special emphasis on the extraction, characterization, and therapeutic use of bioactive compounds of marine and freshwater organisms. It assesses the recent biotechnological tools and methods that make the discovery, isolation, and production of this group of compounds easy, and also finds out the hurdles and prospects of further development of the field. A qualitative systematic review design was decided to be based on secondary data. Data were collected from published literature available in major scientific databases (PubMed, Scopus, Web of Science, ScienceDirect, SpringerLink) between 2020 and 2025. The study synthesized findings from experimental reports, omics analyses, and clinical evaluations. A framework for evaluating the pharmaceutical suitability of aquatic-derived compounds was developed based on compound stability, scalability, sustainability, and clinical evidence. The analysis of results has shown an interesting variety of bioactive substances, where marine ecosystems have presented the greatest diversity, especially in peptides and sulfated polysaccharides. Greener extraction techniques like enzyme-assisted extraction (48-60% yield, high sustainability) and supercritical CO2 (65-82% yield, high sustainability) were pointed out. The research also highlighted the great pharmaceutical prospects of such compounds as marine-derived alkaloids, carotenoids, and collagen peptides. Aquatic bioactive compounds have significant potential in terms of their therapeutic value; nonetheless, in order to achieve this, there are still difficulties in large-scale production and clinical validation. A combination of new biotechnological applications with the study of aquatic biodiversity will hasten the discovery, optimization, and manufacturing of new, sustainable therapeutic agents.