Over the past five decades, ecologists and archaeologists have dismantled two longstanding theoretical constructs. Ecologists have rejected the “balance of nature” concept and archaeologists have dispelled the myth that indigenous people were “in harmony with nature”. Rejection of these concepts poses critical challenges to both fields as current disciplinary approaches are inadequate to grapple effectively with real-world complexities of socioecological systems. In this review, we focus on the relationship between human action and ecosystem change by examining some of the long-term impacts of prehistoric agriculture. Using an interdisciplinary approach, we present results from two studies that suggest that even relatively non-intensive and short-term agriculture can transform ecological systems for a very long time. It is therefore imperative that ecologists and archaeologists work more closely together, creating a truly cross-disciplinary alliance that will help to advance the fields of archaeology and ecology.