Small unmanned aerial systems (UAS) have allowed the mapping of vegetation at very high spatial resolution, but a lack of standardisation has led to uncertainties regarding data quality. For reflectance measurements and vegetation indices (Vis) to be comparable between sites and over time, careful flight planning and robust radiometric calibration procedures are required. Two sources of uncertainty that have received little attention until recently are illumination geometry and the effect of flying height. This study developed methods to quantify and visualise these effects in imagery from the Parrot Sequoia, a UAV-mounted multispectral sensor. Change in illumination geometry over one day (14 May 2018) had visible effects on both individual images and orthomosaics. Average near-infrared (NIR) reflectance and NDVI in regions of interest were slightly lower around solar noon, and the contrast between shadowed and well-illuminated areas increased over the day in all multispectral bands. Per-pixel differences in NDVI maps were spatially variable, and much larger than average differences in some areas. Results relating to flying height were inconclusive, though small increases in NIR reflectance with height were observed over a black sailcloth tarp. These results underline the need to consider illumination geometry when carrying out UAS vegetation surveys.