Flooding is a big homework for the City Government of Samarinda. Flood problems in Samarinda often occur when the rainfall is high even though the duration of the rain is relatively short. This article aims to analyze the sister city cooperation framework model that can be carried out by the city government of Samarinda in dealing with flood problems. The research question in this study is how to design an effective sister city cooperation model and can be used as an attempt to resolve flood problems in Samarinda City. The data collection process in this study used qualitative methods with a literature study approach and interviews with community leaders. The cooperative system framework of the bottom-up model is designed based on the complex interdependence theory by Joseph Nye and Robert Keohane, the authors argued that the collaboration between the Samarinda City Government and transnational actors, supported by active participation from local communities, can be a good collaboration in creating effective solutions related to flood mitigation in Samarinda. The author found that the involvement of the community through socialization and education about the importance of maintaining river ecosystems, mutual cooperation activities in the form of cleaning waterways and drainage, and structuring and relocating residential areas located on the riverbanks, are aspects that play important roles in the process of resolve flood Samarinda City.