Abstract The concept of Resilience Markers has been commonly applied in organizational sciences to identify beneficial markers, behavior or actions that enhance the resilience of a system. However, such frameworks have yet been applied in a Socio-Ecological System framework as an formal investigation of system resilience in an Socio-Ecological System context. Herein, we explore how Resilience Markers can be integrated into an Socio-Ecological System by applying it the case study of the recent shift in agricultural trends in Dadeldhura, Nepal. Through system dynamics modelling, we reveal the provision of irrigation systems to only support profitable, yet drought-vulnerable, vegetable production results an over-reliance on growing cash crops. To mitigate the effects of climate change on the resilience of the agricultural system, we recommend policies in support of the production of diverse drought-resistant cereals crops and promotion of ecological awareness.