Biochar has been proved as a promising and efficient filler in bioretention facilities for enhancing the stormwater pollutants removal. However, the migration behaviors of stormwater pollutants in biochar filled bioretention facilities is unclear. In this study, as one of the most typical stormwater pollutants, naphthalene was selected as an example and a HYDRUS-1D model was first used to understand the migration behavior of naphthalene in a bioretention facility. In comparison with the conventional bioretention soil media (sandy loam), the amended biochar filled bioretention cell showed that the naphthalene removal rate was enhanced by up to 10.1%. Meanwhile, the experimental data was well-fitted by the “two-site sorption model” in HYDRUS-1D model. Another, the effect of rainfall intensity on the naphthalene migration in both bioretention columns was further investigated. The HYDRUS-1D model fitting indicated that the increase in rainfall intensity promoted naphthalene migration by increasing hydraulic conductivity and water flux. In addition, static batch experiments revealed that the biochar filled fillers achieved about 50% higher adsorption capacity than sandy loam. The sensitivity analysis from the HYDRUS-1D model data verified adsorption coefficient Kd and longitudinal dispersivity λ are the main factors affecting naphthalene migration. Finally, the model simulation displays that the proportion of naphthalene retained by the fillers was highest during high rainfall intensities, indicating that the fillers remain the most important fate for naphthalene. This study presents research on the behavior and mechanisms of stormwater pollutant transport through improved bioretention facilities.