Biogeochemical characteristsics of Balikesir-Balya Pb-Zn Mine Waste site, known as the oldest and largest mine tailing site in Turkey, and its influence on generation of acid mine drainage was investigated by 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), and contributing to metal contamination containing up to 1.88 mg/L Pb, 24 mg/L Zn, 2.5 mg/L As ve 17 mg/L Cu. 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 pathways for mobility and redistribution of environmentally important elements into the environments. Based on cultivation based microbiological analysis carried out on acidic ponds developed around and in Balya Mine waste sites, the mean acidofilic sulfur oxidizing bacteria (aSOB) and acidophilic iron oxidizing bacteria were determined as 8.4x10(8)cell/ml ve 9.6x10(7) cell/ml, respectively. The relatively low values for surface water of Maden creek, where mine wastes reach, were determined as 3.8x10(6) cell/ml ve 5.7x10(3) cell/ml, respectively. Molecular analysis of 16S rDNA gene sequences from acidic sediment and sediment from Maden Creek show the dominance of S and Fe-oxidizing prokaryotes belonging to Acidithiobacillus spp. genus in the primary drainage communities. Relatively small populations of Sulfobacillus spp. were also determined. Moreover, species belong to Thiobacillus spp. and Thiovirga spp. genus were only determined on the sediment samples from Maden creek with low acidity relative to acidic sediment. These sulfur 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 sediments of acidic ponds indicate significance of microbial Fe cycle governing mobilization and redistribution of the metals in the waste site. Overall, it is shown that microorganisms regulating S and Fe cycle in Balya mine waste site is the key factors controlling generation and chemistry of acidic drainage water.