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This contribution explores the potential of unmanned aerial systems (UAS) to monitor areas affected by acid mine drainage (AMD). AMD is an environmental phenomenon that usually develops in the vicinity of mining operations or in post-mining landscapes. The investigated area covers a re-cultivated tailing in the Sokolov lignite district of the Czech Republic. A high abundance of AMD minerals occurs in a confined space of the selected test site and illustrates potential environmental issues. The mine waste material contains pyrite and its consecutive weathering products, mainly iron hydroxides and oxides. These affect the natural pH values of the Earth’s surface. Prior research done in this area relies on satellite and airborne data, and our approach focuses on lightweight drone systems that enables rapid deployment for field campaigns and consequently-repeated surveys. High spatial image resolutions and precise target determination are additional advantages. Four field and flight campaigns were conducted from April to September 2016. For validation, the waste heap was probed in situ for pH, X-ray fluorescence (XRF), and reflectance spectrometry. Ground truth was achieved by collecting samples that were characterized for pH, X-ray diffraction, and XRF in laboratory conditions. Hyperspectral data were processed and corrected for atmospheric, topographic, and illumination effects using accurate digital elevation models (DEMs). High-resolution point clouds and DEMs were built from drone-borne RGB data using structure-from-motion multi-view-stereo photogrammetry. The supervised classification of hyperspectral image (HSI) data suggests the presence of jarosite and goethite minerals associated with the acidic environmental conditions (pH range 2.3–2.8 in situ). We identified specific iron absorption bands in the UAS-HSI data. These features were confirmed by ground-truth spectroscopy. The distribution of in situ pH data validates the UAS-based mineral classification results. Evaluation of the applied methods demonstrates that drone surveying is a fast, non-invasive, inexpensive technique for multi-temporal environmental monitoring of post-mining landscapes.