Processes affecting neutralization of acidic coal mine drainage were evaluated within ＇anoxic＇ limestone drains (ALDs). Influents had pH less than or equal to 3.5 and dissolved oxygen < 2 mg/l. Even though effluents were near neutral (pH > 6 and alkalinity > acidity), two of the four ALDs were failing due to clogging. Mineral-saturation indices indicated the potential for dissolution of calcite and gypsum, and precipitation of Al3+ and Fe3+ compounds. Cleavage mounts of calcite and gypsum that were suspended within the ALDs and later examined microscopically showed dissolution features despite coatings by numerous bacteria, biofilms, and Fe-Al-Si precipitates. In the drain exhibiting the greatest flow reduction, Al-hydroxysulfates had accumulated on limestone surfaces and calcite etch points, thus causing the decline in transmissivity and dissolution. Therefore, where Al loadings are high and flow rates are low, a pre-treatment step is indicated to promote Al removal before diverting acidic mine water into alkalinity-producing materials.