Abstract: Biogeochemical characteristsics of Balıkesir-Balya Pb-Zn Mine Waste site, known as the oldest andlargest mine tailing site in Turkey, and its influence on generation of acid mine drainage was investigatedby geochemical, molecular and microbiological approach. The oxidation of sulfide rich rocks and waste,mostly left over from Balya Pb-Zn mining activities, is generating acidic water with low pH (2.7), andcontributing to metal contamination containing up to 1.88 mg/L Pb, 24 mg/L Zn, 2.5 mg/L As ve 17 mg/LCu. Geochemical and molecular/microbiological analysis on mine waste, sediment and water samples(acidic, surface) show that acidic surface waters generated from sulfide weathering are principal pathwaysfor mobility and redistribution of environmentally important elements in the environments. Based oncultivation based microbiological analysis carried out on acidic ponds developed around and in BalyaMine waste sites , the mean acidofilic sulfur oxidizing bacteria (aSOB) and acidophilic iron oxidizingbacteria were determined as 8.4x108cell/ml ve 9.6 x107 cell/ml, respectively.The relatively low values forsurface water of Maden creek, where mine wastes reach, were determined as 3.8 x106 cell/ml ve 5.7x103cell/ml, respectively. Molecular analysis of 16S rDNA gene sequences from acidic sediment and sedimentfrom Maden Creek show the dominance of S and Fe-oxidizing prokaryotes belonging to Acidithiobacillusspp. genus in the primary drainage communities. Relatively small populations of Sulfobacillus spp.werealso determined . Moreover, species belong to Thiobacillus spp.and Thiovirga spp. genus were onlydetermined on the sediment samples from Maden creek with low acidity relative to acidic sediment. Thesesulfur oxidizer indicates a dynamic microbial population which adapt to changing geochemical conditions.Identification of Fe oxidizer and reducer along with Jarosite, plumbojarosite and goethite in the sedimentsof acidic ponds indicate significance of microbial Fe cycle governing mobilization and redistribution ofthe metals in the waste site. Overall, it is shown that microorganisms regulating S and Fe cycle in Balyamine waste site is the key factors controlling generation and chemistry of acidic drainage water.