Indonesia is the third largest fish producer in the world, which contributes to 2.56% of the country’s GDP. Fish farming has contributed to the provision of national protein and food, as well as jobs for local communities. Nevertheless, this sector has contributed to the deterioration of the surface water quality due to discharging of untreated fish farm wastewater into the environment. As the fish farm industry develops, the impact on the environment is also increasing. This research is aimed at developing a sustainable system for removing wastewater pollutants and recovering nutrients from harvesting duckweed biomass, which can be used as a fertiliser or as feedstock for renewable energy production. This proposed research will integrate several aspects of SDGs 6, 7, 11, and 16 to address the environmental issue in Southeast Asia, particularly in Indonesia. To achieve the aims of the project, this study will be conducted in four work packages: WP1 – identification of the most suitable duckweed species for nutrient uptake, WP2 – optimization of nutrient uptake in duckweed biomass, WP3 – analysis of biomethane and biomethanol production from the duckweed biomass, WP4 – transfer of knowledge of sustainable fish farm wastewater management to fish farmers. The outcome of the project will be the implementation of sustainable fish farm wastewater management in the community with concurrent bioenergy production, while the outputs of this study will be published in peer-reviewed journals and disseminated at international conferences.