Emerging contaminants, particularly antibiotics and microplastics (MPs), present significant challenges in wastewater treatment and pose large ecological risks. This study investigates the removal efficiency of sulfamethoxazole (SMX) using Fe-Mn modified biochar (BFM) in fixed bed filtration columns, emphasizing the effect of the presence of polystyrene microplastics (PS-MPs) on SMX behavior in both water (pH ≈ 5.6) and selected wastewater (pH ≈ 8) systems. Batch sorption results show that 10 mg/L SMX in 50 mL water can be completely removed by 100 mg BFM sorbent. The Bed Depth Service Time model indicated the BFM column is feasible for SMX removal in scaled-up continuous wastewater flow operations, while the Yan model best elucidates SMX filtration behavior and suggests the dominant adsorption mechanisms include external mass transfer and intraparticle diffusion. The present of both 20 mg/L and 100 mg/L PS-MPs (pH ≈ 5.6) significantly reduced SMX retention due to competitive sorption. However, at pH 3.2, competitive sorption became negligible due to electrostatic interactions driving the PS-MPs sorption, while neutral charged SMX bound through hydrogen-bonds or π-π EDA interactions. Elevated pH shifted both PS-MPs and SMX sorption to non-electrostatic thus intensifying sorption competition, highlighting the influence of pH on their interaction dynamics. In wastewater, SMX filtration was slightly inhibited by 100 mg/L PS-MPs in BFM columns, whereas PS-MPs removal remained unaffected due to the high ionic strength and alkaline pH. These findings highlight the impact of MPs on pollution removal efficiency in filtration system, essential for enhancing biochar-based wastewater treatment strategies.