This study investigates the spatial variability of soil organic matter (SOM) in the El Maleh sub-watershed (northeastern Algeria), a semi-arid Mediterranean agroecosystem subject to significant soil degradation and erosion pressures. SOM is a fundamental indicator of soil quality, playing a central role in nutrient cycling, carbon sequestration, aggregate stability, and ecosystem resilience. Fifty-two georeferenced composite soil samples were collected from the 0–20 cm horizon using a systematic 1 km × 1 km sampling grid. SOM content was determined by the Walkley–Black wet oxidation method. Spatial structure was characterized through descriptive statistics and ordinary kriging, with a Gaussian semivariogram model selected based on residual sum of squares minimization and leave-one-out cross-validation. Slope and NDVI covariates were incorporated to assess environmental controls on SOM distribution. SOM ranged from 0.302 to 4.401 g/kg, with a mean of 2.274 ± 0.908 g/kg and a coefficient of variation of 40.0%, indicating marked spatial heterogeneity. The Gaussian semivariogram model provided the best fit (nugget = 0.671, range = 14.69 km, SPD = 35.8%), reflecting moderate spatial dependence. Cross-validation confirmed acceptable prediction accuracy (ME = −0.002, RMSE = 0.971 g/kg). Neither slope nor NDVI emerged as significant predictors of SOM distribution (Spearman ρ = 0.186, p = 0.264 and ρ = −0.026, p = 0.858, respectively), with principal component analysis confirming that SOM variability is largely independent of these environmental covariates. The study is limited by the moderate sampling density (52 points over 521 km²), the absence of seasonal monitoring, and the restriction to SOM as the sole soil quality indicator. These findings provide the first spatially explicit SOM baseline for the El Maleh sub-watershed, supporting soil conservation planning and sustainable land management in semi-arid Mediterranean agroecosystems.