Acid mine drainage flowing from an underground seep, through an anoxic drain to an oxidation pond and then trickling filter was distributed among three treatment ponds for manganese reduction before releasing the mining water to a surface stream. Manganese was more effectively removed from the integrated green algae and microbial mat with limestone substrate pond (algae mat system) than from control ponds containing limestone or pea gravel substrates without mat. Although there was some Mn-cell binding, manganese was primarily deposited as precipitates at the pond bottom. Day/night and winter/summer manganese removal was essentially the same. The greater efficiency in Mn removal by the algae mat pond was most pronounced with higher flow rates and during the night. At 2 metres from the influent point of each pond, the algae mat pond removed 2.59 g manganese/day/M2, respectively, compared to 0.80 in the limestone pond and 0.37 in the pea gravel pond. Control ponds showed either Mn breakthrough or near breakthrough (Mn outflow releases > US Environmental Protection Agency regulations of 2 mg/L) during night-time sampling or when mine drainage flow exceeded 4.5 L/min.