Successful mitigation of flood risk requires an integrated, basin-wide approach. This is particularly important in transboundary river basins, where the actions of multiple stakeholders must be coordinated. The Ciliwung River, Indonesia, presents an example of a complex urban basin that crosses multiple administrative borders. The increasing frequency and severity of floods in the downstream capital city of Jakarta has highlighted the need for better river governance arrangements. However, it is unclear what form these arrangements should take. This paper aims to develop a conceptual framework that identifies the key concepts relevant to flood management and governance in transboundary river basins and how they relate to the situation in the Ciliwung. Key concepts were drawn from a review of the literature conducted using online databases and search engines. The framework firstly outlines the flood hazard itself in terms of drivers and impacts. It then goes on to establish the associated governance arrangements and identifies any interdependencies. The framework highlights multiple interrelated drivers of flood risk, both human and physical. There is also a range of governance issues related to capacities, coordination of institutions, and fragmentation of plans and policies. Due to flood risk and river management complexities, this conceptual framework provides much-needed clarity to develop improved management arrangements in the Ciliwung River Basin. It also sets a framework to facilitate future research on transboundary management in relation to flood risk in other urban and peri-urban river basins.