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Monitoring of mine waste on sulphide deposits through remote-sensing hyperspectral data contributes to the prediction of potential surface-water quality, quantitatively estimating acid drainage and metal contamination on a yearly basis. Based on previous Hymap mapping of salt efflorescence on mine wastes, various domains within the mine facilities (Iberian Pyrite Belt, Spain), selected because of their geomorphological setting, were sampled to conduct a laboratory experiment. Samples from mine-waste piles, pyrite mud tailings and river sediments were continuously exposed to the atmosphere during the summer, and spectral measurements were collected in the dark room on several days. The spectral response was monitored throughout the summer, when the pyrite oxidation process is active and the mineralogy on the surface changes continuously. The mineralogical identification capability of algorithms such as the Spectral Angle Mapper, Binary Encoding and Spectral Feature Fitting based on archive spectral libraries is discussed. Trends of mineral growth differ spectrally over time according to the geological setting. Subtle mineralogical changes are described using the spectral response and their meaning as indicators of pyrite oxidation intensity on mine-waste piles, pyrite mud tailings and river sediments. Therefore, sulphide mine-waste weathering products may be used as small-scale targets for a short-term record of climate variability, providing a useful tool to assess environmental geological indicators in semi-arid areas.