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Mapping invasive vegetation species in arid regions is a critical task for managing water resources and understanding threats to ecosystem services. Traditional remote sensing platforms, such as Landsat and MODIS, are ill-suited for distinguishing native and non-native vegetation species in arid regions due to their large pixels compared to plant sizes. Unmanned aircraft systems, or UAS, offer the potential to capture the high spatial resolution imagery needed to differentiate species. However, in order to extract the most benefits from these platforms, there is a need to develop more efficient and effective workflows. This paper presents an integrated spectral–structural workflow for classifying invasive vegetation species in the Lower Salt River region of Arizona, which has been the site of fires and flooding, leading to a proliferation of invasive vegetation species. Visible (RGB) and multispectral images were captured and processed following a typical structure from motion workflow, and the derived datasets were used as inputs in two machine learning classifications—one incorporating only spectral information and one utilizing both spectral data and structural layers (e.g., digital terrain model (DTM) and canopy height model (CHM)). Results show that including structural layers in the classification improved overall accuracy from 80% to 93% compared to the spectral-only model. The most important features for classification were the CHM and DTM, with the blue band and two spectral indices (normalized difference water index (NDWI) and normalized difference salinity index (NDSI)) contributing important spectral information to both models.