Low impact development (LID) practices contribute to the reduction of flooding and improvement of water quality. Water crises may be a result of water scarcity and flooding due to climatic changes and the increase of impervious areas, and thus, stormwater harvesting becomes a sustainable alternative solution for relative water problems. The performance of a bioretention system with the submerged zone (SZ) and unsaturated zone (USZ) was evaluated as an alternative for stormwater harvesting. The study was carried out on a laboratory scale, using a bioretention box to simulate the processes that occur in a real system and in the field. The system was efficient in removing TP (68.5% and 76.5%), COD (71.6% and 56.9%), and (28% and 16.6%) in USZ and SZ events, respectively. removal (31%) occurred only at SZ events. was exported at all events tested but at values below the Brazilian CONAMA Resolution 357/2005 on the quality of water bodies for supply. The bioretention effluent showed relatively high values of turbidity; however, the pH parameter presented good values in all experiments ( and ), and E. coli only in some cases presented satisfactory values to meet the Brazilian Standard for Rainwater Usage for nonpotable purposes (). In general, both configurations provide different improvements for stormwater to support sustainable water resources management. This study presents a comparison between bioretention systems with and without SZ as an initial proposal for the improvement in bioretention systems in Brazil; however, more experiments must be monitored, and new improvements should be tested for reaching restrictive water reuse purposes.