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The exposure of metal sulfides to air or water, either produced naturally or due to mining activities, can result in environmentally damaging acid mine drainage (AMD). This needs to be accurately monitored and remediated. In this study, we apply high-resolution unmanned aerial system (UAS)-based hyperspectral mapping tools to provide a useful, fast, and non-invasive method for the monitoring aspect. Specifically, we propose a machine learning framework to integrate visible to near-infrared (VNIR) hyperspectral data with physicochemical field data from water and sediments, together with laboratory analyses to precisely map the extent of acid mine drainage in the Tintillo River (Spain). This river collects the drainage from the western part of the Rio Tinto massive sulfide deposit and discharges large quantities of acidic water with significant amounts of dissolved metals (Fe, Al, Cu, Zn, amongst others) into the Odiel River. At the confluence of these rivers, different geochemical and mineralogical processes occur due to the interaction of very acidic water (pH 2.5–3.0) with neutral water (pH 7.0–8.0). This complexity makes the area an ideal test site for the application of hyperspectral mapping to characterize both rivers and better evaluate contaminated water bodies with remote sensing imagery. Our approach makes use of a supervised random forest (RF) regression for the extended mapping of water properties, using the samples collected in the field as ground-truth and training data. The resulting maps successfully estimate the concentration of dissolved metals and related physicochemical properties in water, and trace associated iron species (e.g., jarosite, goethite) within sediments. These results highlight the capabilities of UAS-based hyperspectral data to monitor water bodies in mining environments, by mapping their hydrogeochemical properties, using few field samples. Hence, we have demonstrated that our workflow allows the rapid discrimination and mapping of AMD contamination in water, providing an essential basis for monitoring and subsequent remediation.