This paper describes a new methodology to map intertidal sediment using a commercially available unmanned aerial system (UAS). A fixed-wing UAS was flown with both thermal and multispectral cameras over three study sites comprising of sandy and muddy areas. Thermal signatures of sediment type were not observable in the recorded data and therefore only the multispectral results were used in the sediment classification. The multispectral camera consisted of a Red–Green–Blue (RGB) camera and four multispectral sensors covering the green, red, red edge and near-infrared bands. Statistically significant correlations (>99%) were noted between the multispectral reflectance and both moisture content and median grain size. The best correlation against median grain size was found with the near-infrared band. Three classification methodologies were tested to split the intertidal area into sand and mud: k-means clustering, artificial neural networks, and the random forest approach. Classification methodologies were tested with nine input subsets of the available data channels, including transforming the RGB colorspace to the Hue–Saturation–Value (HSV) colorspace. The classification approach that gave the best performance, based on the j-index, was when an artificial neural network was utilized with near-infrared reflectance and HSV color as input data. Classification performance ranged from good to excellent, with values of Youden’s j-index ranging from 0.6 to 0.97 depending on flight date and site.