Research has argued that enhanced local capacity is important for tackling global change problems. Yet, in practice, many sustainability challenges fail to gain traction due to limited local capacities for policy implementation. Our project will explore this knowledge-practice gap by investigating institutional conditions at the municipal level that shape the implementation of transboundary river policies. We will focus on two municipalities in the vulnerable upstream of Citarum River, Indonesia, one of the most heavily polluted in the world. The government has promoted an integrated approach although with limited implementation success. We will adapt a leapfrogging framework—developed as a transdisciplinary tool to capture relevant barriers and enablers and involve local stakeholders in action research, comprising interviews and participatory workshops, to co-develop visions, strategies, and capacities to implement the revitalisation policies. Our project will generate insights into municipal capacities for addressing transboundary challenges while developing socio-ecological resilience. It will enhance scientific collaboration between Indonesia and Australia, whilst generating transferable evidence and tools for characterising the institutional dimensions of transboundary environmental governance, and how it may be enhanced from the bottom up to support more sustainable environmental management approaches across other degraded river systems in the Asia-Pacific regions.