Both sand and fly ash were found to be promising for phosphorus removal in bioretention systems. However, nutrient removal in bioretention systems with sand, soil and fly ash was still uncertain due to a lack of data about the influence of layer structure and submerged zone. In this study, a mixture with sand, soil and fly ash (1:1:1) was selected as the base in bioretention systems with different packed layer structures and heights of submerged zone. The comparison of multi-layered structure with mixed structure implied that the used bioretention system with multi-layered structure was superior to that with mixed structure for nitrogen and phosphorus removal. The investigation of the influence of submerged zones on nutrient removal indicated that the submerged zone could significantly improve nitrate removal efficiency with 67.52%-86.32%, while sharply reduce the removal of ammonia nitrogen (from 95.15% to 51.81%) and TP (from 88.66% to 44.50%). Overall evaluation of the effect of packed layer structures and submerged zones suggested that the bioretention system with multi-layered structure at the height of submerged zone at 20-40cm was the most satisfactory, due to its microbial environment.