This review explores the transformative potential of aquatic biorefineries in advancing sustainable resource utilisation. As global demands for renewable resources intensify, biorefineries have emerged as versatile solutions. Focusing on aquatic environments, this paper delves into diverse biomass resources, encompassing microorganisms, algae and aquatic plants. It navigates through key biorefinery processes, including hydrothermal liquefaction, algae cultivation and enzymatic conversion, illuminating their roles in sustainable biofuel and high-value chemical production. Thermochemical conversion processes, such as pyrolysis and gasification, offer additional pathways for bio-based product generation. The review critically assesses challenges in these processes, ranging from technical intricacies to regulatory considerations. Examining products derived from aquatic biorefineries (i.e. biofuels, chemicals and biomaterials) underscores their versatility. Looking ahead, the paper identifies technical challenges, regulatory landscapes and emerging technologies as focal points for future research. The review concludes by envisioning aquatic biorefineries as key players in sustainable resource management, advocating for research and technological innovation to propel this transformative field into the mainstream of the bio-based economy.