This study aims to formulate an integrated and sustainable management strategy for Lake Limboto’s sustainable ecosystem. The stages of the study include (1) identifying the problems that occur in Lake Limboto and analyzing the general conditions of the ecosystem, which includes biophysical waters, land use patterns in water catchment areas, and socio-economics; (2) measuring the sustainability of the lake management using the Multi-Dimensional Scaling (MDS) method and leverage analysis. The results of the Multi-Dimensional Scaling analysis show that the sustainability index value of the ecosystem, economic, social, institutional, and technological dimensions are less sustainable, less than 50. In contrast, the economic dimension is entirely sustainable at 62.90; meanwhile, the ecosystem dimension index is 18.59, which means the sustainability status is poor. These figures indicate that the management of Lake Limboto and its surrounding area mainly considers the economic aspects and relatively ignores the dimensions of its ecosystem.