The interest in sustainable bioenergy solutions has gained great importance in Europe due to the need to reduce GHG emissions and to meet environmental policy targets, not least for the protection of groundwater and surface water quality. In the Municipality of Solrød in Denmark, a novel bioenergy concept for anaerobic co-digestion of food industry residues, manure and beach-cast seaweed has been developed and tested in order to quantify the potential for synergies between climate change mitigation and coastal eutrophication management in the Køge Bay catchment. The biogas plant, currently under construction, was designed to handle an annual input of up to 200,000t of biomass based on four main fractions: pectin wastes, carrageenan wastes, manure and beach-cast seaweed. This paper describes how this bioenergy concept can contribute to strengthening the linkages between climate change mitigation strategies and Water Framework Directive (WFD) action planning. Our assessments of the projected biogas plant indicate an annual reduction of GHG emissions of approx. 40,000t CO2 equivalents, corresponding to approx. 1/3 of current total GHG emissions in the Municipality of Solrød. In addition, nitrogen and phosphorous loads to Køge Bay are estimated to be reduced by approx. 63tyr.-1 and 9tyr.-1, respectively, contributing to the achievement of more than 70% of the nutrient reduction target set for Køge Bay in the first WFD river basin management plan. This study shows that anaerobic co-digestion of the specific food industry residues, pig manure and beach-cast seaweed is feasible and that there is a very significant, cost-effective GHG and nutrient loading mitigation potential for this bioenergy concept. Our research demonstrates how an integrated planning process where considerations about the total environment are integrated into the design and decision processes can support the development of this kind of holistic bioenergy solutions.