Policy makers concerns for post-2013 CAP create significant interest in the investigation of alternative CAP scenarios impacts on rural areas. Capturing complex economic, social and environmental interactions associated with changes in the CAP requires a holistic and integrated approach. Hence, a system dynamics model integrating agriculture, environment, rural economy and human resources is developed and applied in a typical Greek rural area. Model results indicate that alternative CAP paths could generate very different rural impacts, depending on the territorial characteristics of the rural region. This supports the conclusion that policy makers should considerably take regional specificities into account when designing agriculture and rural development policy interventions.