Best management practice (BMP) in drainage ditch systems is of high concern due to its importance in intercepting and removing pollution. Biochar has recently become an interesting option for agricultural pollution elimination, but knowledge is still limited on the fate of nitrogen (N) in drainage ditch systems with biochar added into the sediment. This isotope tracer study examined the effects of biochar addition into the sediment on the fate of inorganic N (15N-NO3- and 15N-NH4+) in sediment microcosms through a 93 day incubation experiment. Four types of sediment microcosm (sediment only, sediment + biochar, sediment + plant, sediment + biochar + plant) were set to investigate N migration and transformation using 15N pool dilution. The results indicated that 0.75% biochar addition significantly increased sediment pH and water holding capacity by 0.29 and 2.6%, respectively. Biochar addition suppressed sediment 15N-N2O emissions and decreased 15N uptake by Calamagrostis angustifolia. From the 15N distribution in different sediment layers, it was found that biochar may increase the risk of N leaching and speed up its downward mobility. Meanwhile, 15N fate was affected by the planting of Calamagrostis angustifolia, exhibiting reduced leakage and residue in sediment. Vegetated microcosms suppressed N2O emissions, as the Calamagrostis angustifolia effectively competed with microbes and utilized N for its own growth and development. Therefore, Calamagrostis angustifolia could be beneficial in the removal of agricultural non-point source nitrogen pollution as a potential option for BMP.