This paper examines the challenges of and facilitating strategies for linking disaster risk reduction (DRR) and climate change adaptation (CCA) in addressing urban floods, drawing from Indonesia’s experience. The fragmentation between efforts to implement DRR and CCA leading to unnecessary duplication could increase confusion at both the community and wider governance levels and reduce the effectiveness of urban flood management. Through the lens of collaborative governance, this paper analyzes the barriers for integrating DRR and CCA and options to better align their practices in the context of a megapolitan city, Jakarta, Indonesia. The key findings of this study confirmed that institutional fragmentation, in concert with inconsistent facilitation and collaboration mechanisms, were the strongest barriers to aligning DRR and CCA action. The absence of accountable leadership was a key impediment for successful partnership-building processes to support political and technical collaboration. Leadership in these contexts plays an important role in (1) developing sustainable relationships, (2) convincing potential stakeholders to collaborate, (3) persuading partners to commit to sharing resources, and (4) agreeing/sharing a common vision of the partnership actions needed to mitigate harm and reduce urban vulnerability. These factors are critically important for reducing the direct and indirect impacts of flooding in Jakarta. Such lessons from Indonesia on linking DRR and CCA offer valuable insights to inform the development of policies and strategies to deal with urban floods for global cities faced with similar challenges.