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The accelerated climate crisis has exacerbated the existing water and soil management challenges in the Mediterranean region, which are usually attributed to the combination of both irrational irrigation and unsustainable farming practices. The current conditions and future projections indicate that water-related risks are expected to intensify during the coming decades. Moreover, farmers often do not possess high environmental awareness; they adopt non-sustainable farming practices such as the extensive use of herbicides instead of mowing/mulching for the weeds, thus affecting soil hydraulic characteristics and fertility. To investigate the effects of different weed-management practices on soil organic carbon and thus on soil water holding capacity and infiltrability, an extensive soil-sampling campaign was performed in the semi-arid Mediterranean agricultural pilot basin of Agia—Greece. The pilot is located in the Pinios river basin, which constitutes the most highly productive agricultural plain in the country. The Agia basin was selected since it presents the uneven spatiotemporal distribution of groundwater resources and the wide application of herbicides, while an urgent need exists to sustain and improve agricultural production, with the main crops being apples and cherries. Moreover, the Agia basin constitutes a highly instrumented area where the Pinios Hydrologic Observatory belonging to the International Long Term Ecological Research network has been developed, and thus additional field measurements could contribute to the overall data-collection framework. Soil sampling was conducted in apple orchards in April 2022, just before the beginning of the growing season. Ninety six soil samples in total were collected from eight different fields; half of them applied systematic herbicides treatment, and others mulching. For the upper soil profile (0–10 cm depth), the results indicate that soil organic carbon in the fields applying mowing was found to be higher by more than 30% compared to the fields applying herbicides. The corresponding difference for soil depth of 10–30 cm was 7%, thus demonstrating the effectiveness of mulching in increasing soil organic carbon. The results of the current study could be upscaled at a larger scale in the context of adapting agricultural water-stressed regions to climate change, whilst contributing significantly to the production cost and the preservation of the ecosystemic values of the regional nexus. [ABSTRACT FROM AUTHOR]