Several ongoing projects are harvesting maritime biomass from the Baltic Sea for eutrophication mitigation and utilisation of the recovered biomass. Some of this biomass comprises common reed (Phragmites australis), one of the most widespread vascular plants on Earth. Reed utilisation from eutrophied coastal areas needs to be evaluated. Therefore, a system analysis was performed of reed harvesting for biofuel and biofertiliser production. The specific objectives of the analysis were to: investigate the methane yield associated with anaerobic co-digestion of reed; make a primary energy assessment of the system; quantify Greenhouse Gas (GHG) savings when a fossil reference system is replaced; and estimate the nutrient recycling potential of the system. The results from energy and GHG calculations are highly dependent on conditions such as system boundaries, system design, allocation methods and selected indicators. Therefore a pilot project taking place in Kalmar County, Sweden, was used as a case study system. Laboratory experiments using continuously stirred tank reactor digesters indicated an increased methane yield of about 220 m³ CH₄/t volatile solids from co-digestion of reed. The energy balance for the case study system was positive, with energy requirements amounting to about 40% of the energy content in the biomethane produced and with the non-renewable energy input comprising about 50% of the total energy requirements of the system. The net energy value proved to be equivalent to about 40 L of petrol/t reed wet weight. The potential to save GHG emissions compared with a fossil reference system was considerable (about 80%). Furthermore an estimated 60% of the nitrogen and almost all the phosphorus in the biomass could be re-circulated to arable land as biofertiliser. Considering the combined benefits from all factors investigated in this study, harvesting of common reed from coastal zones has the potential to be beneficial, assuming an appropriate system design, and is worthy of further investigations regarding other sustainability aspects.