Biofilters are an effective treatment option for the substantial heavy metal loads in urban stormwater. However, to increase their nitrogen treatment efficacy, the introduction of a submerged (anoxic) zone (SZ) and a cellulose based carbon source (C) has been recommended because it has been shown to enhance denitrification and thereby increase overall nitrogen removal. To examine the impact of this design modification on heavy metal treatment, a laboratory study using biofilter mesocosms with different levels of SZ and with or without added C was conducted. The results show that SZ and C have a significant impact on metal treatment. In particular, the removal of Cu was improved significantly. The presence of SZ and C allows outflow Cu concentrations to meet Swedish and Australian water quality guidelines, which are not met with a standard biofilter without SZ or C. Although Zn and Pb removal was enhanced slightly by the presence of a SZ, this improvement is of less practical importance, since Zn and Pb removal is already very high (>95%) in standard biofilters. The best metal treatment was achieved with 450 and 600 mm SZ. Based on these results, the incorporation of SZ with C in stormwater biofilters is recommended.