Bioretention can reduce surface runoff, slow down peak flow, and delay peak time by increasing the infiltration capacity of the underlying surface. The media structure directly affects the performance of bioretention systems. Four pilot tanks with different media configuration were built, and hydraulics and water volume reduction were studied though intermittent, simulated storm events. The results showed that water volume and peak flow reduction rate were the most stable and efficient for #1 (fly ash mixing sand, 1:1 by volume) than other systems, which were 58.6%–67.9% and 72.0%–86.4%, respectively. Partial least squares regression (PLS) was used to build a model for the relation between water volume reduction rate and its influencing factors (R2 = 0.76), and the factors that influence bioretention water volume reduction were ranked from strongest to weakest as follows: infiltration rate (IR) > submerged area height (SAH) > inflow volume (IV) > antecedent dry time (ADT). In addition, volume reduction rate exhibited a positive correlation with ADT and SAH, and a negative correlation with IR and IV. Three water transfer simulations with different infiltration rates were conducted using HYDRUS-1D under designed inflow conditions, and the minimum relative error is obtained for #1.