Limestone is commonly used for neutralization of acid mine drainage (AMD). Its main advantages are its lower price, sustained generation of alkalinity and production of low sludge volumes. Nevertheless, armouring of limestone by ferric hydroxides is a problem in oxic limestone drains and in active limestone treatment systems, reducing the efficiency of the process. Due to these disadvantages, there is a permanent search for cheaper and more effective neutralization agents. Many alkaline industrial wastes are gaining importance in the treatment of AMD. The possibilities to use two different industrial by-products, red mud from a bauxite exploitation and low grade magnesium hydroxide from a magnesite mine, as neutralizing and bacterial inhibiting agents, and the comparison with conventional limestone treatment has been studied in this paper. An AMD from Rio Tinto mine site with an initial pH of 2.4 and a ferric concentration of 1 g/L was used. Comparative test were done percolating the AMD in a continuous form with a peristaltic pump through three different columns filled with limestone, red mud and low grade magnesite, during one month and in same conditions of flow rate and amount of each compound used to fill the columns. The evolution of pH, iron and heavy metals, sulphates and microbial populations in the percolate were monitored at different times. The results showed that the best neutralization capacity was obtained with low grade magnesite during the month treatment. By contraire limestone and red mud loosed their neutralization capacity after 10 and 13 days respectively. The control of microbial populations showed that there is an inhibition of chemolithotropic bacteria as long as the materials maintain their neutralization capacity, reverting to the initial conditions when this capacity was loosed.