Population growth and rapid urbanisation increase the consumption of resources such as phosphorus as fertiliser for agri-food production, and increase the adverse environmental impacts on water resources such as lakes. The PhD research particularly addresses the increasing challenges on eutrophication in lakes and depletion of phosphorus resources for agri-food systems in the context of a sustainable circular nutrient economy. The main objective of the research project is to holistically assess and quantify the sustainability performance of integrating a nutrient recovery system on wastewater and water resource management, using Laguna de Bay, Philippines as the geographical boundary. Moreover, a pilot-scale nutrient recovery reactor was installed at Salikneta Farm, Philippines, wherein an alternative phosphorus fertiliser was recovered from septage and sewage. The recovered fertiliser was then applied locally in the farm, providing evidence of the circularity of the proposed system. Hence, the novelties of the research are the integration of acid hydrolysis as pretreatment of septage to maximise phosphorus recovery, the installation of a pilot-scale nutrient recovery reactor that is the first in the Philippines, and the life cycle sustainability assessment (LCSA) of nutrient recovery from domestic wastewaters considering the three sustainability pillars: environmental, economic, and social. The life cycle assessment results show that the integration of nutrient recovery provided environmental benefits and improvement in freshwater eutrophication, terrestrial ecotoxicity, water consumption, and mineral resource scarcity. The social life cycle assessment results also provided preference for the proposed nutrient recovery from wastewaters with respect to the stakeholder categories while the life cycle cost is PhP 86,936.05/m³. Through LCSA, the proposed nutrient recovery from domestic wastewater scenario has the highest sustainability performance. Results generally imply policy review for septage management, system optimisation, and evaluation of alternative methods of wastewater management, in terms of life cycle thinking and sustainability across the globe.