The diatom Didymosphenia geminata ("Didymo") forms thick and dense mats under low-nutrient and high-shear conditions. To investigate the effects of Didymo on open-channel hydraulics, we collected cobbles covered with Didymo mats from the Waitaki River, Canterbury, New Zealand. The cobbles were then emplaced in a recirculating flume and the system hydraulics were observed under several imposed flow rates. Following these measurements, the Didymo mats were removed from the cobbles, and the measurements were repeated over the bare cobbles. The mats overlapped and bridged gaps between cobbles, and thus were expected to reduce form drag. However, shear velocities and friction factors increased when Didymo mats were present, indicating that Didymo-covered beds are hydraulically rougher than the cobble beds despite the fact that the cobble surface is smoothed by the presence of the mats. We conclude that the mats introduce an additional roughness scale, and that their surface is much rougher than the bare stones. This conclusion is supported by direct visual observations of the mat morphology.