The study area (Algarve) is located near the Eurasia–Africa plate boundary, experiencing significant tectonic and seismic activities. Regional geology is characterised by the presence of Mesozoic and Miocene carbonate rocks which are affected by karst phenomena. This karst is covered by terrigenous sediments of Upper Miocene and Pliocene–Pleistocene age. In the study area, the Pliocene–Quaternary cover deposits are affected by a large number of mesoscopic structures, including joints, faults, and a few folds, which indicate neotectonic activity. However, these sediments also present similar structures that result from underground karst evolution, raising the need to differentiate the neotectonic structures from those of non-tectonic origin. In fact, a variety of ductile, semi-brittle and brittle structures develop in the sediments that fill up the karst wells, controlled by different rheological behaviour of the cover deposits, various strain rates associated with sudden collapse or progressive sinking, and the variable shape of the karst pits walls. The structure’s geometry, geographical dispersion and directional scattering were used as criteria to infer a non-tectonic genesis. It is discussed whether some karst related structures may be controlled by the contemporary tectonic stress field and consequently are interpreted in the regional geodynamical framework.