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Aeolian processes in drylands often transcend into sand encroachment, a common form of land degradation. Highly reflective desert features, hence sandy areas, often cause spectral confusion, and mapping through remote sensing techniques can be challenging. This work aims at designing an efficient classification method that minimises spectral confusion of desert features, hence two types of sandy areas. Moreover, we employ land cover (LC) change detection over the last 30 years. The extraction and spatiotemporal variations of LC and sand encroachment areas in the Dahar-Jeffara Medenine site (southeastern Tunisia) are assessed by employing Landsat imagery (1984 and 2014), a 30 m digital elevation model of Shuttle Radar Topography Mission (SRTMGL 1 arc second), field data and X-ray diffraction analyses of sand samples. Five new spectral indices were designed and employed in a Decision Tree (DT) classifier for the extraction of 11 LC classes, including two different types of sandy areas. The DT map yielded an overall accuracy of around 89%. Change detection results showed substantial change in several landscape components and an increase of sand units by 29% within the Jeffara-Medenine plain over the last three decades. Geomorphological observations and multi-temporal, spectral and mineral analyses indicate a main, possible in-situ source area of sand.