River basins are unique dynamic systems that depend on their natural hydrologic variability and streamflow diversity to provide a wide range of ecosystem services. However, on a global scale, the fragmentation of river networks and the dampening of environmental variability are increasing by the unforeseen pressures of climate change and anthropogenic disturbances, including unsustainable water withdrawals, dam constructions, and land-use change. These disturbances can accumulate, pushing the system beyond a threshold, inducing a regime shift, and leading the system to an alternative state. But how much forcing a river basin can take until the system undergoes a regime shift and into an alternative state? And how to assess ecological resilience of a river basin from anthropogenic and climatic disturbances? A resilience approach seeks to explain these dynamics, including understanding the ecosystem organization and functional flow traits that are inherently bound to the system’s adaptive capacity to maintain critical functions and processes during changing environmental conditions. In this work, I propose a tractable framework to evaluate the ecological resilience of river basins by assessing three measurable resilience attributes: alternative regimes, thresholds, and adaptive capacity using the transboundary Rio Grande - Bravo basin as a case study. The broader impact of this work is to advance into the general endeavor of moving forward from the theoretical understanding of resilience into a more tangible and quantifiable measure to assess it. But most importantly is the strong potential that this framework has to support conservation efforts, ecosystem management and inform current policy of river basins to understand and incorporate the inherent dynamism of ecosystems into water management.