Belowground plant parts play an important role in wetland functioning but their biomass and structural traits have remained out of focus in constructed wetlands. We studied the biomass and structural traits of rhizomes and roots of Phragmites australis (Cav.) Steud. in the inflow and outflow parts of a newly established constructed wetland with subsurface horizontal flow (Slavošovice, Czech Republic). The rhizome biomass of P. australis increased until the 6th year after planting and reached about 1.5 and 2.0 kg.m−2 in the inflow and outflow parts of the bed, respectively. The average live root biomass was about 7% of the total live belowground biomass. Analysis of the rhizome branching pattern showed that in the 8th year after planting, the rhizome life span was definitely two years and most probably up to four years. The root structural traits showed that thicker and shorter roots were formed in the inflow part. As a result, there were differences in total root length, which reached 2.4 km m−2 in the inflow and 3.3 km m−2 in the outflow parts. This probably reflects a higher nutrient availability at the inflow rather than the toxicity of the discharged wastewater. The results of this study support previous arguments that the belowground parts of P. australis are an important carbon source in constructed wetlands, tolerate the anaerobic environment in the treatment bed well and provide a large surface area for the attachment of microorganisms.