Management of nutrient inputs and usage of nuisance biomass as feedstock for bioenergy may be the solution of coastal lagoons eutrophication. We studied the species composition, photosynthetic pigments (Chl-a and Chl-c) and performance (OJIP-kinetics and JIP-test parameters), biochemistry (lipids and carbohydrates composition), and hydrogen production potential of Limnoraphis (Lyngbya) nuisance biomass collected from Lafri lagoon (1.24 km(2)) in Greece. The results showed that the removal of algal biomass from Lafri lagoon before its sedimentation, characterized by low F nu/Fm (0.42) and PItotal (2.67) values, and transfer of this in a simple, closed bioreactor, has the potential to produce hydrogen (H-2), a renewable CO2-neutral energy that can directly be converted into electricity. The free carbohydrates of the lagoon water and that from the algal cells (42g glucose analogs per m(3)) could be also transferred to alcohols (biofuels), while the rest of the biomass could be used as organic fertilizer. The total lipid content (2.51%) of dry biomass composed primarily by palmitic acid was low. However, the presence of eicosapentaenoic (3.5%), and docosahexaenoic (1.7%), polyunsaturated fatty acids is worth mentioning. By harvesting and conversion of this coastal lagoon nuisance algal biomass to energy or other products, one could improve its water quality and, therefore, biodiversity and fish production; that is a sustainable solution of eutrophication necessary for the ongoing climatic change.