This paper discusses how a Geodesign method facilitates a process of managing a closed-loop urban system through algae cultivation by turning urban waste streams into renewable energy. The method informs six stages of processes for designing an algae-powered urban system: objective model, representational model, performance model, scenario model, evaluation model and decision model. Three sites in Atlanta were tested to explore to what extent the system performance can move toward a “net-zero” urban environment. The results show that the three neighborhoods have the highest potential to reach 12–18% of the total building energy demand met by the energy production in the algae system in the extreme scenario. Other renewable energy resources need to be added and more efforts of building energy reduction need to be made to move the performance of urban system closer to “net-zero”.