The existence of multilayered boundaries and networks in a river basin redefines the river basin geographies and concepts and poses extreme challenges to centralized notions of Integrated River Basin Management (IRBM). The paper traces various boundaries that exist due to the physical peculiarities, political situations, resource transfer scenarios and socio-economic networks in one of the most exploited river basins in the highly populated biodiversity hotspot of the Southern Western Ghats in India and analyses the implications for IRBM. The coexistence of multiple, dynamic and often overlapping boundaries existing within and beyond the hydrological boundary encompasses an inclusive region of resource engagement coined as 'inclusive basin' which embeds in it various communities of interests. The governance in such an 'inclusive basin', heavily mediated by the power gradients of the boundaries involved, can be envisaged as an issue-based polycentric approach which incorporates these interest group domains at multiple scales. The paper attempts a critical examination of the multilayered boundaries that connect the natural hydrographic basin to its physical, social and political settings and their influence on natural resources management, conservation and conflict resolution, especially in the light of the National River Linking Project.