Excess nitrogen and phosphorus in domestic wastewater accelerate eutrophication, yet many biochar-based nutrient studies remain dominated by batch tests with limited evidence under continuous-flow conditions relevant to real treatment units. Magnesium-activated biochar was packed into laboratory-scale columns and operated under continuous flow while systematically varying bed depth (25 vs 50 cm) and hydraulic configuration. Treatment performance was monitored through influent–effluent nutrient measurements over extended operation, supported by hydraulic assessment (hydraulic retention time, permeability via Darcy analysis) and surface characterization using SEM before and after filtration. Across all configurations, Mg²⁺-activated biochar removed ammonium effectively, with peak removal of 76.69–79.15% achieved within 8–9 days of operation across all four configurations, followed by a partial decline (overall trial means ranging 37.91–56.29% depending on configuration). The best-performing setup (50 cm, downflow–upflow) reached the highest single-day removal of 79.15% (46.58 mg/L) on day 8 and the highest overall mean removal (56.29% ± 15.28%) across the trial. In contrast, phosphate removal was strongly configuration-dependent: the 25 cm downflow configuration sustained stable removal (65.03% ± 10.29%) throughout the trial, while the remaining three configurations showed unstable behavior, with effluent concentrations frequently exceeding influent values, suggesting desorption/leaching and/or biologically mediated accumulation, and underscoring the importance of filter configuration as an operational control. Hydraulically, the system achieved an estimated HRT of ~16 h at 25 mL/min, and thicker media exhibited higher permeability (0.001161 vs 0.000714 cm/s). SEM revealed substantial pore blockage and fouling after operation, consistent with coupled physical filtration and chemical adsorption processes. Overall, Mg²⁺-activated biochar filtration shows strong promise for ammonium polishing with clear configuration-dependent performance gains, while phosphate management requires targeted operating strategies to prevent desorption and enable reliable recovery under continuous flow.