Sulfide wastes from the extraction of metal ores generate acidic mine drainage (AMD), containing toxic elements such as arsenic (As), antimony (Sb) and thallium (Tl). Remediation processes using microbial communities have been developed to remove these pollutants from AMD, but the biological processes involved in these treatments still need to be controlled to ensure their effectiveness. The scientific obstacles, which are the subject of the thesis, lie in (1) a lack of knowledge on direct and indirect microbial transformations of Sb and Tl, and (2) for As, a weak understanding of relationships that exist between dynamics of microbial communities, their functional potential, water physico-chemistry and efficiency of treatments applied to AMD. A multidisciplinary approach, mainly based on microbial ecology and physico-chemistry tools, allowed to characterize the diversity of microbial communities capable of directly or indirectly transforming As and Sb at increasing experimental scales: batch reactor, laboratory continuously fed systems, and pilot on site. A microbial consortium able of tolerating up to 100 mM of antimonite and oxidizing it under acidic conditions (pH