Fluvial systems offer a challenging and varied environment for topographic survey, displaying a rapidly varying morphology, vegetation assemblage, and degree of submergence. Traditionally, theodolite- or global positioning satellite-based systems have been used to capture cross-section and breakline-based topographic data, which have subsequently been interpolated. Advances in survey technology have resulted in an improved ability to capture larger volumes of information with infrared terrestrial and aerial Lidar systems capturing high-density (<0.02 m) point data across terrestrial surfaces. The rise of structure from motion (SfM) photogrammetry, coupled with small, unmanned aerial vehicles (sUAV), has the potential to record elevation data at reach scale subdecimeter density. The approach has the additional advantage over Lidar of seeing through clear water to capture bed details and also generating orthorectified photographic mosaics of the survey reach. However, data accuracy has yet to be comprehensively assessed. We present a survey protocol for sUAV deployment and provide a reach scale comparison between a theodolite and SfM sUAV survey on the River Sprint at Kendal, the River Ehen at Egremont, England, and the Afon Elwy at Llanfair Talhaiarn, Wales. Comparative analysis between theodolite survey and SfM suggests similar accuracy and precision across terrestrial surfaces with error lowest over solid surfaces, increasing with vegetation complexity. Submerged SfM data captured bed levels generally to within ±0.25 m at depths of <2.4 m, with only a weak relationship recorded between error and flow depth. Significantly, associated error when linked to channel D50 highlights the ability of unmanned aerial vehicles to capture accurate fluvial data across a range of river biotopes and depths to 2.4 m.