Mine-impacted water bodies are considered to be one of the most serious threats to the environment. These can be highly acidic and often contain elevated concentrations of sulfate and soluble metals. The microbial generation of H2S by reduction of more oxidized sulfur species, and consequent precipitation of metal sulfides, known as biosulfidogenesis, is a promising technology for remediating acid mine drainage (AMD). The objective of this work was to develop an integrated system for remediating a target AMD at an operating mine in northern Brazil using a single low pH anaerobic sulfidogenic bioreactor (aSRBR) and an aerobic manganese-oxidizing bioreactor. A synthetic version of the mine water, which contained 7.5 mM copper and lower concentrations (< 0.25 mM) of other transition metals (Zn, Ni, Co and Mn) was used in the experimental work. In the first stage, H2S generated in the aSRBR was delivered to an off-line vessel containing synthetic AMD, which removed > 99% copper (as CuS) while no co-precipitation of other metals was apparent. The partly-processed AMD was then dosed with glycerol and fed into the aSRBR where zinc, nickel and cobalt were precipitated. The effect of varying the pH and temperature of the bioreactor was examined, and > 99% of Ni, Zn and Co were precipitated in the aSRBR when it was maintained at pH 5.0 and 35ºC. The bacterial communities, which were included 4 species of acidophilic sulfate-reducing bacteria, varied in composition depending on how the bioreactor was operated, but were both robust and adaptable, and changes in temperature or pH had only short-term impact on its performance. Manganese was subsequently removed from the partly-remediated synthetic AMD using upflow bioreactors packed with Mn(IV)-coated pebbles from a freshwater stream which contained Mn(II)-oxidizers, such as the bacterium Leptothrix discosphora and a fungal isolate belonging to the order Pleosporales. This caused soluble Mn (II) to be oxidised to Mn (IV) and the precipitation of solid-phase Mn (IV) oxides. Under optimised conditions, over 99% manganese in the processed AMD was removed. Metal sulfides (ZnS, CoS and NiS) that had accumulated in the aSRBR over 2 years of operation were solubilised by oxidative (bio)leaching at low pH. With this, ~ 99% Zn, ~ 98% Ni and ~ 92% Co were re-solubilised, generating a concentrated lixiviant from which metals could be selectively recovered in further downstream processes. The use of methanol and ethanol either alone or in combination with glycerol were evaluated as alternative electron donors for biosulfidogenesis. Methanol was not consumed in the bioreactor, though sulfate reduction was not inhibited in the presence of up to 12 mM methanol. In contrast, ethanol was readily metabolised by the bacterial community and sulfate reduction rates were relatively high compared to glycerol. Two acidophilic algae were characterised and their potential to act as providers of electron donors for biosulfidogenesis was also evaluated. Although algal biomass was able to fuel sulfate reduction in pure cultures of aSRB and in the aSRBR, rates were much lower than when either glycerol or ethanol were used.