River restoration in urbanising contexts faces multiple pressures and increased governance complexities. The aspiration for basin-scale policy integration has been widely promoted but is not well tested in urbanising rivers and implementation success remains disjointed across jurisdictions. We link the multi-level governance lens with the notion of place to facilitate a deeper examination of the unique assemblages of socio-material configurations that embed restoration practices across locations. Employing an embedded qualitative case study of the Citarum revitalisation in Indonesia, where a territorialised military operation co-existed with multi-level arrangements, we show that variability, rather than consistency, of governance approaches persisted across geographies. The variabilities were shaped by different place-based conditions – critical in influencing restoration practices and governance processes – such as place leadership, attachment to river, neighbourhood stewardships, issue-based networks and a sense of legitimacy. Thus, our study challenges the normative primacy of the basin-scale integration in existing water governance research and policy, while offering a more robust and critical approach towards gathering place-based insights and in situ evidence of governance complementarity and inconsistency.