Bioretention basins are frequently subjected to anaerobic conditions, which can create an optimum environment for microbial activities to remove nitrogen (N) and sequester carbon (C) in the below-ground filter media. However, these biological processes are associated with the potential production of greenhouse gas (GHG) emissions that need to be measured. In this study, we quantified nitrous oxide (N2O), methane (CH4) and carbon dioxide (CO2) fluxes from the soil under a transition period from dry to wet conditions in subtropical Australia. The GHG fluxes were measured on the bed of slow (wet basin) and fast (dry basin) draining basins and their embankment area. In addition, the influence of Carex appressa plant on emissions was investigated. Finally, the denitrification potential of the basin soil and their C and N accumulation (over an 18-month interval) were measured. The dry and the embankment soils were both slight sinks of CH4 (−16 and − 2 μg CH4 − C m−2 h−1) while being a high source of CO2 (> 520 × 103 μg CO2 − C m−2 h−1). In comparison, the wet basin was a source of CO2 and CH4 with a mean value of 123× 103 μg CO2 − C m−2 h−1 and 2405 μg CH4 − C m−2 h−1, respectively. The dry and wet basins were a slight source of N2O emissions and were positively driven by precipitation. The presence of C. appressa plant increased CH4 consumption and N2O generation. The results suggest that adopting a slow-draining design for bioretention systems, such as lowering the hydraulic conductivity and/or provision of a saturation zone higher in the soil profile, can reduce CO2 and N2O fluxes from the soils and potentially improve water quality performance of these basins. However, an increase in CH4 fluxes should be the expected by-product.