Stormwater biofiltration systems (also known as biofilters, bioretention, rain gardens) are engineered nature-based solutions, which help mitigate aquatic nitrogen pollution arising from storm runoff. These systems are being increasingly used in a range of climates across the world. A decline in treatment performance is frequently observed in cold weather conditions. While plant species comprise an important design factor influencing system performance, the effect of temperature on the fate of dissolved nitrogen forms, namely ammonium (NH4+) and nitrate (NO3-), in the presence of different plant species in these systems remains unclear. A large scale laboratory experiment was undertaken that measured potential rates of nitrification, denitrification and dissimilatory nitrate reduction to ammonium (DNRA) as well as the microbial community structure to investigate nitrogen fate and hence removal under two different temperature conditions (2 °C and 15 °C) in the presence of four distinct plant species. The results indicate that lower nitrification rates (reduced by a factor of 4) coupled with potential media NH4+ desorption could be contributing to reduced NH4+ removal during cold conditions. Planting with species exhibiting good nutrient uptake capacity can reduce the extent of this performance decline. While NO3- reduction generally remains problematic during cold weather (<0 to 55% reduction), which may not be significantly different from warmer periods, the study demonstrated that the denitrification potential and gene abundance (nap, nar, NirS, norB, nosZ) to be higher than those of nitrification (amoA). Denitrification may not proceeding at optimal rates due to lack of conducive environmental conditions. Nitrogen transformation via DNRA was found to be relatively insignificant. Future studies should investigate the potential of employing cold-resilient plant species to maintain both NH4+ and NO3- removal in cold weather conditions.