Stormwater biofilters are dynamic environments, supporting diverse processes that act to capture and transform incoming pollutants. However, beneficial water treatment processes can be accompanied by undesirable greenhouse gas production. This study investigated the potential for nitrous oxide (N2O) and methane (CH4) generation in dissolved form at the base of laboratory-scale stormwater biofilter columns. The influence of plant presence, species, inflow frequency, and inclusion of a saturated zone and carbon source were studied. Free-draining biofilters remained aerobic with negligible greenhouse gas production during storm events. Designs with a saturated zone were oxygenated at their base by incoming stormwater before anaerobic conditions rapidly re-established, although extended dry periods allowed the reintroduction of oxygen by evapotranspiration. Production of CH4 and N2O in the saturated zone varied significantly in response to plant presence, species, and wetting and drying. Concentrations of N2O typically peaked rapidly following stormwater inundation, associated with limited plant root systems and poorer nitrogen removal from biofilter effluent. Production of CH4 also commenced quickly but continued throughout the anaerobic interevent period and lacked clear relationships with plant characteristics or nitrogen removal performance. Dissolved greenhouse gas concentrations were highly variable, but peak concentrations of N2O accounted for <1.5% of the incoming total nitrogen load. While further work is required to measure surface emissions, the potential for substantial release of N2O or CH4 in biofilter effluent appears relatively low.