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Agricultural runoff is a major cause of degradation to freshwater sources. Nitrate is of particular interest, due to the abundant use of nitrogen-based fertilizers in agricultural practices globally. This study investigated the nitrate removal of biochar produced from an agricultural waste product, macadamia nutshell (MBC). Kinetic experiments and structural analyses showed that MBC pyrolsed at 900 °C exhibited inferior NO3− removal compared to that pyrolsed at 1000 °C, which was subsequently used in the column experiments. Concentrations of 5, 10 and 15 mg/L, with flowrates of 2, 5 and 10 mL/min, were examined over a 360 min treatment time. Detailed statistical analyses were applied using 23 factorial design. Nitrate removal was significantly affected by flowrate, concentration and their interactions. The highest nitrate removal capacity of 0.11 mg/g MBC was achieved at a NO3− concentration of 15 mg/L and flowrate of 2 mL/min. The more crystalline structure and rough texture of MBC prepared at 1000 °C resulted in higher NO3− removal compared to MBC prepared at 900 °C. The operating parameters with the highest NO3− removal were used to study the removal capacity of the column. Breakthrough and exhaustion times of the column were 25 and 330 min respectively. Approximately 92% of the column bed was saturated after exhaustion.