Acid mine drainage (AMD) is produced by weathering and microbial oxidation of pyrite exposed to infiltrating water and air in mine waste rock, tailings, and mine excavations. One strategy for remediation of AMD sources is initiation of a shift in microbial populations from dominance of iron oxidizing bacteria that propagate AMD formation to iron and sulfur reducing microorganisms by the addition of biodegradable organic matter. This thesis describes an investigation of the influence of hydrologic conditions in waste rock formations on AMD formation and carbon addition as a remediation technique. Experiments were conducted using two 37.8-liter tanks packed with rock particles obtained from a mine waste pile near Leadville, CO. One tank was run under water saturated conditions. The second was run with unsaturated water flow (∼16% saturation). Production of acidity, soluble ferric iron and sulfate in the Unsaturated condition was significantly higher than in the Saturated system. Both functional populations were larger in the Unsaturated mode indicating that conditions were more optimal for both populations. Evidence corroborates that heterotrophs are supported by the primary production of the iron oxidizers. After acid generating conditions were established, glucose was added to the tanks at increasingly higher loading rates (from 0.25g/day to 12 g/day). Lower levels of glucose induced water chemistry changes in the Saturated condition (pH increased 2.5 to 4.7) compared to the Unsaturated condition. In the Unsaturated mode higher carbon loading was required for demonstrable changes in water chemistry. pH increased from 1.5 to 4.5, but only after several months of 10-12g carbon and 5% tryptic soy broth addition per day. A clear shift in functional populations away from iron oxidizing toward heterotrophic, iron reducing, and sulfate reducing metabolisms was demonstrated in both flow conditions. A rapid increase in pH to above 6 in both conditions occurred after carbon/nutrient addition was stopped. Higher pH conditions lasted for at least 75 days after carbon addition ceased. AMD generation resumed several days earlier in the Unsaturated condition. Results indicate that drainage flow controls the formation of AMD and influences the effectiveness of carbon addition as a remediation technique.