This paper presents initial efforts to establish the San Juan Urban Long-Term Research Area Exploratory (ULTRA-Ex), a long-term program aimed at developing transdisciplinary social-ecological system (SES) research to address vulnerability and sustainability for the municipality of San Juan. Transdisciplinary approaches involve the collaborations between researchers, stakeholders, and citizens to produce socially-relevant knowledge and support decision-making. We characterize the transdisciplinary arrangement emerging in San Juan ULTRA-Ex as a knowledge-action network composed of multiple formal and informal actors (e.g., scientists, policymakers, civic organizations and other stakeholders) where knowledge, ideas, and strategies for sustainability are being produced, evaluated, and validated. We describe in this paper the on-the-ground social practices and dynamics that emerged from developing a knowledge-action network in our local context. Specifically, we present six social practices that were crucial to the development of our knowledge-action network: 1) understanding local framings; 2) analyzing existing knowledge-action systems in the city; 3) framing the social-ecological research agenda; 4) collaborative knowledge production and integration; 5) boundary objects and practices; and 6) synthesis, application, and adaptation. We discuss key challenges and ways to move forward in building knowledge-action networks for sustainability. Our hope is that the insights learned from this process will stimulate broader discussions on how to develop knowledge for urban sustainability, especially in tropical cities where these issues are under-explored.