Olive mill wastewater (OMWW), a by-product of the olive oil industry, poses significant environmental challenges due to its high content of organic pollutants, suspended solids, and phenolic compounds. Uncontrolled disposal, especially from small-scale mills, can result in soil degradation and water pollution. This study proposes an innovative fixed-bed column filtration system employing olive mill solid waste-derived biochar (BC) and raw olive stone (OS) as low-cost adsorbents for OMWW treatment. Biochar was produced from OMSW through pyrolysis at 585 °C, yielding a material with a high BET surface area (258.72 m²/g), notable microporosity (115.58 m²/g), and substantial external surface area (143.14 m²/g). Both BC and OS were packed into separate filtration columns and tested under identical flow conditions (1 mL/min) to assess their comparative removal efficiency of pollutants. The results revealed that biochar significantly outperformed olive stone in removing key contaminants. After two successive filtrations using BC, removal efficiencies reached 91.6% for total suspended solids (TSS), 68.5% for mineral matter (MM), 73.5% for total phenolic compounds (TPC), and 76.4% for chemical oxygen demand (COD). In contrast, OS filters exhibited lower performance across all parameters. The concentration of TPC decreased from 6.8 g/L in raw OMWW to 1.8 g/L after BC filtration. Kinetic modeling using the Thomas, Bohart–Adams, and Yoon–Nelson models provided a reliable fit to the experimental data, offering insight into adsorption dynamics and column performance. This comparative study demonstrates the superior potential of OMSW-derived biochar as a sustainable and efficient material for environmental separation processes. The fixed-bed column system not only enables the valorization of agricultural waste, but also contributes to eco-friendly wastewater treatment practices in olive oil-producing regions.