Raw algae waste naturally thrown on shores could pose serious threats for landfilling and its reuse for composting or further processing as added-value by-products require knowledge-based decisions and management for the sustainable development of local ecosystems. Raw marine waste containing salt (halite) and heavy metals that eventually accumulate in algae hamper their safe applicability in soil fertilization or in other exploitations. Here, the suitability of algal biomass for use as an environmentally safe fertilizer was investigated, thereby supporting sustainable coastal management. The simple extraction of the dry algal biomass of three abundant Mediterranean species, Enteromorpha intestinalis, Corallina elongata, and Gelidium pulchellum, in water containing sodium carbonate resulted in a greenish extract containing a reduced heavy metals content, and nutrients such as K+, PO43−, SO42−, NO3−, Ca2+, and Mg2+. UV-Vis and Raman techniques, including surface-enhanced Raman scattering (SERS), were employed for the fast evidencing of polyphenols, carotenoids, and chlorophylls in the extracts content, while E. intestinalis extract additionally exhibited polysaccharide signals. Heavy metals analysis showed that the major metals in the extracts were Fe, Ni, Zn, and Cu; however, their levels were an order of magnitude lower than in the dry biomass. The extracts also showed a mild antibacterial effect. The combination option of aqueous extracts with powdered crustacean shells to obtain a novel, eco-friendly, solid biofertilizer complex was further shown, which could be pelleted for convenient use. The immersion of solid biofertilizer pellets in water is accompanied by re-solubilization of the compounds originating from algae extracts, presenting the opportunity for dry storage and easier handling and land applicability. In summary, aqueous extracts of marine algae waste present an environmentally safe and attractive way to recycle excessive algal biomass and to formulate a new, eco-friendly biofertilizer complex.