Sandy desert ecosystems of Central Asia are highly vulnerable to climate change, land degradation, and increasing anthropogenic pressure, yet the soil conditions supporting native desert vegetation remain insufficiently characterized. This study investigates soil development and physicochemical properties under the canopy of Calligonum aphyllum across different geomorphological conditions in the southern Balkhash region of Kazakhstan. Field investigations were conducted within the Ili River delta, where nine soil profiles were described across three geomorphological settings. Soil samples were analyzed using standard soil analytical methods to assess particle-size composition, soil organic matter, nutrient availability, carbonate content, salinity, and sodicity indicators. The studied soils were predominantly sandy, with sand fractions ranging from 88 to 96% and very low clay content, resulting in weak horizon differentiation, high permeability, and limited water-retention capacity. Soil organic matter and total nitrogen contents were consistently low across all sites. Available phosphorus decreased with depth, particularly in carbonate-enriched horizons, whereas exchangeable potassium remained comparatively high. Total salinity was low, with chloride–sulfate and calcium–sodium dominance, and no evidence of sodicity was observed based on SAR values. Clear differences among geomorphological settings were identified, including relatively homogeneous sandy substrates, dust-enriched semi-stabilized sands, and actively reworked aeolian ridges. The results indicate that C. aphyllum can persist under nutrient-poor, coarse-textured sandy conditions and is associated with surface root concentration, local substrate stabilization, and early soil-profile differentiation. These findings highlight the ecological importance of C. aphyllum in sandy desert habitats and provide site-specific soil information relevant to vegetation-based restoration and sustainable land management in arid regions of Central Asia.