<p>Weathering of sulphur-bearing rocks leads to acid rock drainage (ARD), which decreases water pH, mobilizes heavy metals, and forms coloured coatings of metal precipitates on riverbeds. This study assessed the effects of ARD on microbial biofilm biodiversity and community structure in alpine streams across two Pyrenean regions (Núria and Chistau). Biofilms were sampled from acidic (pH &lt; 5.5) and non-acidic (pH &gt; 6.5) streams, and at their confluence, where metal precipitates occur (white-coated streams). We characterised bacterial and eukaryote communities by molecular tools and specifically analysed the diatom communities by morphology approach. Their respective community composition varied with stream category for both bacteria and eukaryotes, but only bacteria exhibited a loss in diversity in acidic and white-coated streams. Diatom communities and diversity differences were driven mainly by region. In acidic and white-coated streams, bacteria which can use metals and sulphurs in their metabolic processes increased, together with fungi and some photosynthetic groups (<i>Chlorophyta</i>, <i>Streptophyta</i>) among eukaryotes. Amplicon Sequence Variants (ASVs) assigned to acidophilic and psychrotolerant bacteria were highly associated with acidic streams, and <i>Cyanophyceae</i> ASVs were highly associated with white-coated ones. As for eukaryotes, ASVs of <i>Chrysophyceae</i> were associated with both acidic and white-coated streams. Nonetheless, the regional factor remained consistently significant across microbial communities. This study indicates that ARD-affected streams can support microbial communities adapted to their extreme conditions, with the communities in white-coated rivers differing markedly from those in acidic rivers.&#xa0;</p>