Biofiltration systems, as one of the best management practices, have good potentials to improve stormwater quality and hydrology of urban catchments. While biofiltration systems are well-studied in developed countries, the majority of those studies are conducted for temperate climate and there is a lack of lab-scale and field-scale studies on such systems under tropical conditions. This paper focuses on the performance of a lab-scale prototype biofiltration systems in stormwater retention efficiency as well as pollutants removal (including heavy metals and nutrients) from synthetic stormwater reproducing tropical rainfall events. A three-layer sand-based filter media with two different native plants including Pedilanthus tithymaloides and Cyperus alternifolius was selected for this study. Results showed that the system with Cyperus has a better stormwater retention capacity compared to the one with Pedilanthus. In addition, the observed infiltration rate in Cyperus and Pedilanthus were 338 mm/h and 267 mm/h, respectively. The better hydraulic performance in the system with Cyperus was attributed to the deeper and more extensive root penetration of this plant (as deep as 800 mm) compared to Pedilanthus (as deep as 250 mm). While both systems failed to perform well in removing total nitrogen, they performed significantly better in removing total phosphorus (Cyperus and Pedilanthus removed 67.3% and 62.5% of total phosphorus, respectively). The statistical analysis of results showed that the top 100 mm layer of filter media is the main contributor to total phosphorus removal. However, no major differences were observed between the two systems in phosphorus removal. Moreover, both systems were also capable of removing the available heavy metals (i.e., Fe, Cu, Mn, Ni, Pb, and Zn) as the removal efficiencies exceeded 90%, except for Fe (76%). Similar to phosphorus, it was concluded that the top layer is the major contributor to the heavy metals removal. Overall, the biofiltration system using Cyperus was found to be a successful system for operating under tropical conditions.