The absence of large archaeological settlements in the Eastern Arabian Peninsula suggests that most of the recent wet periods occurring during climate oscillations in these areas were short-lived. However, a ∼ 2-by-3-km buried rectangular feature was discovered opportunistically in the southeast of the Qatar Peninsula while performing radar subsurface mapping of structural conduits for groundwater characterization. The feature is characterized by its unique contrasting patterns of surface and subsurface roughness as well as its organic-rich mixture of soils, as assessed from high-resolution radar and multispectral observations, respectively, and validated with GPR and EM subsurface probing. The above characteristics could be the only remaining evidence for a large primitive settlement due to the harsh erosive setting. To explore the natural or anthropogenic origin of this anomalous feature, we compare its dimensions, structural setting, roughness, and composition to similar formations in the Qatar Peninsula and other arid karst environments. Findings suggest that the feature is texturally and compositionally unique within the Qatar Peninsula, and is not reproduced in other arid karst terrains nor reproduced by the fracture patterns associated with the Qatar-South Fars Arch. We hypothesize that the feature is a karst depression modified by semi-stationary primitive human settlements ∼ 3640 BP or earlier based on radiocarbon dating of in-situ charcoal samples. Moreover, the organic-rich mixture of soil and the occurrence of several symmetrical features observed inside the perimeter suggest that landscaping, farming and irrigation activities could have occurred within the site, further suggesting that long-lasting wet conditions—with sufficient fresh water resources or reliance on karst aquifers—were able to sustain a relatively large primitive settlement not previously witnessed in the region’s archaeological record. Future improvements in the resolution and coverage of orbital L-band radar observations, as used above, can provide new insights into understanding prehistoric human occupation under fluctuating climatic conditions and groundwater dynamics in these hyper-arid regions.