The introduction of a saturated zone (SZ) has been recommended to address the issue of nitrogen removal fluctuation in the bioretention system, which is one of the most versatile low-impact development facilities for urban stormwater management. Nine experimental columns were used to characterize the nitrogen concentration variations over the outflow during wetting periods and in SZ during the antecedent drying periods (ADPs), as well as compare removal efficiencies of various nitrogen species in systems with different SZ depths under alternate drying and wetting conditions. Results indicated that NO3−-N concentrations in the outflow showed quasi-logistic curve-shaped variations over time: being low (<0.5 mg/L) in the early process, sharply increasing thereafter, and finally flattening around 3.0 mg/L with NO3− leaching; NH4+-N and organic nitrogen (ON) concentrations were consistently low around 0.5 mg/L and 1.8 mg/L, respectively during the wetting periods. NH4+ removal efficiency in bioretention systems was consistently high around 80%, not varying with the increasing SZ depth; ON removal efficiency had a slight rise from 57% to 84% and NO3− removal efficiency was significantly enhanced from −23% to 62% with the SZ depth increasing from 0 to 600 mm. Deeper SZ could store more runoff and promote more denitrification of NO3− and mineralization of ON during the ADPs, providing more “old” water with low NO3− and ON concentrations for water exchange with “new” inflow of higher NO3− and ON concentrations during the wetting periods. The total nitrogen (TN) removal, a combined result of the instantaneous removal through adsorption and retention in the upper soil layer during the wetting periods and the gradual removal via denitrification and mineralization in SZ during the ADPs, was also improved by increasing the SZ depth; TN removal efficiency was elevated from 35% to 73% when the SZ depth increased from zero to 600 mm.