Acid and metalliferous drainage (AMD) occurs when sulphidic minerals, such as arsenopyrite, chalcopyrite and pyrite, are exposed to oxygen and water. Climate, geology and mine site practices can have a significant impact on AMD composition. The elemental composition of the AMD can also affect the bacterial community. Our hypothesis was that in the dry season the AMD at two mine sites, Rum Jungle and Mt Todd, in the Northern Territory, Australia, has a higher concentration of dissolved metals because standing water evaporates during the extended dry period. Our second hypothesis was that the wet and dry season bacteria community in AMD at Rum Jungle and Mt Todd are different, and this difference is correlated to seasonally specific changes in physicochemistry. The first hypothesis was tested by measuring elemental concentrations in AMD during the wet and dry seasons at Mt Todd and Rum Jungle mine sites. The physicochemical properties such as temperature, pH and dissolved oxygen were also measured. To test the second hypothesis, we extracted DNA from AMD samples collected at Rum Jungle and Mt Todd during the wet and dry seasons. The hypervariable V6 region of the bacterial 16S rRNA gene was sequenced by 454 pyrosequencing. The bacterial community composition was examined and related to physiochemical variables. The elemental concentrations in Rum Jungle AMD were higher in the dry season compared to the wet season, but at Mt Todd the elemental composition of AMD changed with year, rather than season. The bacteria community in AMD at Rum Jungle changed between the wet and dry season while in Mt Todd AMD the bacteria community from year 1 was significantly different from year 2. The data showed that the elemental composition and bacteria communities of AMD at Rum Jungle and Mt Todd are influenced by season, mine site practices and geological characteristics of the ore body. In addition, the iron oxidising bacteria Leptospirillum and Acidithiobacillus typically associated with AMD in temperate regions were not prevalent at out tropical study sites.