The concept of resilience has been rapidly accepted across multiple disciplines and spheres of applied work, but operationalizing resilience poses several methodological challenges. Issues associated with complexity due to system dynamics, nonlinearity, and self-organization render traditional evaluation methods insufficient and often speculative. Focusing on system actors, processes and structures, and the scales of the system involved, we provide a framework and methodology to establish evidence and evaluate resilience. We take the case of two transboundary communities situated in the Gangetic plains of South Asia, i.e., Paklihawa (Nepal) and Shivpur (India), that are affected by annual monsoonal floods. Using an accessibility-based livelihood framework, we identified key indicators contributing to resilience and measured them in select households, pre- and post-monsoon, over three consecutive years. Focusing on the variation in well-being and coping capacity, we recommend two propositions that must simultaneously be satisfied for increased resilience. Over time, first, the well-being of the communities should increase, and second, the magnitude of recovery from shocks by the communities should decrease, approaching zero. We used a repeated measures analysis of variance to evaluate the significance of changes in well-being and recoveries over time. Our analysis shows that the resilience of Paklihawa increased significantly while Shivpur's remained inconclusive. The two propositions and the methodology are robust to a wide range of shocks and social-ecological systems. This study contributes to the growing need for approaches toward measuring resilience and the monitoring and evaluation of resilience-focused interventions.