Accelerated climate crisis exacerbates existing water and soil management challenges in Mediterranean region which are usually attributed to the combination of both irrational irrigation and unsustainable farming practices. Current conditions and future projections indicate that water-related risks are expected to be intensified during the coming decades. Alongside, farmers often present not high environmental awareness; adopting non-sustainable farming practices such as an extensive use of herbicides instead of mowing/mulching for the weeds; this way affecting soil hydraulic characteristics and fertility. To investigate the effects of different weed management practices on soil organic matter content and therefore, 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 Pinios river basin that constitutes the most highly productive agricultural plain of the country. The Agia basin was selected since it presents uneven spatiotemporal distribution of groundwater resources and wide application of herbicides, while an urgent need exists to sustain and improve apples production. Moreover, the Agia basin constitutes a highly instrumented area where the Pinios Hydrologic Observatory belonging to 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 8 different fields; half of them applying systematic herbicides treatment, and others mulching. For the upper soil profile (0-10 cm depth), the results indicate that soil organic matter in the fields applying mowing was found to be higher by more than 20% 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 matter. 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.