The presence and activities of microbes on and within minerals have profound worldwide environmental and economical consequences; from the consumption of atmospheric carbon dioxide during biotically-enhanced weathering of basalt, to the degradation of manmade structures and microbial mineral formation. In metal mineral mines, microbial activities have both positive and negative consequences. Microorganisms reside on minerals, including sulfide ores such as pyrite and chalcopyrite, abundant mine ores in the UK and worldwide. Through microbial metabolism of the iron contained within these ores, sulphuric acid is produced, resulting in an acidic mine environment. Drainage from such mines enter watercourses and wetlands, producing acid mine drainage (AMD). In addition, toxic heavy metals such as lead, are more soluble at a lower pH and are thus usually present in AMD, adding to the environmental concern. While some of the common microbial species found in such mines have been well characterised, there remains significant questions regarding microbial communities as a unit, and their functioning, such as: i) are communities established quickly and do the species within those communities change over time, ii) which species are active and what are they doing, and iii) what effect does mineral chemistry (mineralogy), have on the structure and functioning of the communities. In answering these questions we take a step closer to reducing environmental impacts, through increased awareness of how human activities impact on the microbial activities and the resulting AMD produced. This research will answer the questions outlined above, using Parys mine in Wales, as the study site; a prime example of abandoned metal mines and once the world’s largest producer of copper. Two of the most abundant primary ores in the mine, chalcopyrite, and sphalerite will be the minerals of focus, with additional analyses of pyrite and galena, and the secondary minerals jarosite and pisanite.