Denitrification beds, utilising fragmented wood particles as the carbon source, have been successfully used to remove nitrate from point source discharge. Other more labile carbonaceous solids have provided higher short-term nitrate removal rates than wood in laboratory scale trials, but the longevity of these media is unproven. In addition, the nitrate removal rate of a bed is indicated to be temperature dependent. Improving the hydraulic efficiency of a denitrification bed, by reducing short-circuit flow, may also provide for increased long-term nitrate removal rate and reduced bed size and lower installation cost. In this study, we compared the hydraulic properties and hydraulic efficiency of nine carbon media, including five grain sizes of wood particles, in 0.2 m3 barrels, at two temperatures (14 °C and 23.5 °C). The relationship between hydraulic efficiency and nitrate removal of the different media was also investigated. We found that carbon substrate and temperature were more influential on nitrate removal rate than hydraulic efficiency of the media. While larger grain-sizes of wood media were less hydraulically efficient than smaller grain-sizes, the difference in hydraulic efficiency was small. We also found that primary porosity of the wood media increased with temperature, which may have been caused by contraction of the wood particles with increasing temperature due to loss of water from the cellulose to the liquid phase. While hydraulic properties and hydraulic efficiencies varied between carbon media, the variation did not cause significant difference in nitrate removal rate. The results indicate that future work on improving nitrate removal performance of denitrification beds should focus on carbon availability of the substrate and increasing bed temperature, rather than on identifying more hydraulically efficient media.