Biochar is anticipated to be an effective option for mitigating nitrogen (N) leaching and improving the hydraulic characteristics of soil, particularly sandy soil. However, little attention has been paid to understanding the effect of biochar on N leaching and hydraulic conductivity (K) in fine-textured soil. Additionally, whether different biochar application methods have different effects on N leaching and K remains unclear. Therefore, our objective in this study is to determine the effects of biochar with different application methods on nitrate/ammonium leaching and K in silty clay soil. The three biochar application patterns were as follows: A, biochar was mixed into 0–10 cm of surface soil; B, biochar was mixed into 10–20 cm of subsurface soil; and C, biochar was mixed evenly into 0–20 cm of plow layer soil. In addition, biochar was added at three rates, namely, 1%, 2% and 4% (mass ratios), and a soil column without biochar addition served as the control (CK). Our results demonstrated that the choice of biochar application method significantly influenced N leaching and soil K and balance between
the soil K and N leaching, particularly for nitrate. Additionally, the leaching of N in silty clay soil occurred mainly in nitrate form. Compared with the CK, all 1% biochar treatments increased nitrate leaching (except C1%, which showed no differences from the CK) and tended to decrease K. However, all 4% biochar treatments increased nitrate leaching due to a high K. All 2% biochar treatments significantly reduced nitrate leaching by 8.3–17.0%, and B2% significantly increased the saturated hydraulic conductivity (Ksat) of soil by 20.9%. Hence, the mixing of biochar at a rate of 2% into the subsurface soil effectively mitigated N leaching and increased K in silty clay soil. These findings could have some implications for the field application of biochar. For instance, the combination of subsurface biochar application with that of fertilizer to roots in orchards or with deep tillage in fields, which would mimic the B2% model, would yield multiple benefits, including lower costs.