Acid mine drainage (AMD) discharge, particularly from the North Eastern Coalfield (NEC), Assam, has been a major persistent ecological threat. A lab-scale constructed wetland (CW) deriving organic wastes as the wetland media was implemented to treat high acidity (724 mg L–1 as CaCO3) AMD loaded with sulfate (1000–1300 mg L–1). Metal contents in mine wastewater comprised iron, aluminium, manganese, zinc, cobalt, nickel and chromium as 104, 25, 6.2, 5.1, 1.1, 1.1 and 1.1 mg L–1, respectively. CW operated continuously at a hydraulic loading rate (HLR) of 0.03 m3 m–2 d–1 for 282 days. Effluent water quality was monitored, and resulting shifts in microbial diversity were identified. Results demonstrated 771 mg L–1 (as CaCO3) alkalinity in effluent and metal removal (87–100%), except Co and Mn, which surpassed effluent discharge criteria. Further, the high-throughput sequencing results revealed significant reformations in bacterial assemblages throughout the operational period. Proteobacteria (45%) and Bacteroidetes (26%) represented the major bacterial groups at the start-up of CW, which later declined due to the elimination of aerobic strains under anaerobic conditions. Additionally, methanogenic archaea suppressed greatly due to the competition from sulfate and iron-reducers. An increase in the relative abundances of key functional bacteria (Firmicutes, Bacteroidetes, Actinobacteria and Acidobacteria) in the treatment phase indicated stable operation. Sulfate reduction (62%) was partial, evidenced by the prominence of sulfate-reducing bacteria (SRB) (Thermodesulfobium, Syntrophobacter, Desulfomonile and Desulfovibrio). This study offers insights into the microbial dynamics within an organic-media-amended CW, which directly influences AMD treatment.