<p>Large areas in the arid Southern Levant are dotted with ancient agricultural terraces and runoff harvesting installations. In the Negev Highlands, Israel, they were constructed in the 3rd–4th centuries CE, maintained for 6–7 centuries, and then abandoned after the 10th century. Their design pattern and foundations provide a rare insight to the prevailing environmental conditions during the middle Holocene, while their 600–700 years cultivation tells the story of their maitainance and desert agriculture in these regions. From their abandonment onwards, they documented more than 1000 years of land degradation and soil erosion till present time. In this paper, we follow a complete cycle of desert agriculture of two sites near the UNESCO world-heritage town of Avdat. We reconstruct the landscape at the period pre-dating the first anthropogenic intervention, through the centuries of cultivation, and into a millennium of abandonment until the present erosion phase. We use high-resolution 3-D data to document the erosion and environmental dynamics during these two millennia, and to compute rates of siltation and erosion. Long-term measures of such kind are unique, as it is rare to find a millennium-scale documentation of soil erosion processes. Their study improves our understanding of the long-term environmental change mechanism acting in arid environments. The detailed analysis of these installations also offers insights into methods for soil conservation, for sustainable desert inhabitation, and for strategies to protect world-heritage installations. As the globe-wide struggle to combat soil erosion becomes urgent, this case study becomes even more relevant.</p>