Accelerated pollution of rivers and streams because of human activity are a concern throughout the world. The objective of this study was to assess the impact of coal mine drainage on streams of Jaintia hills, Meghalaya, India. The water quality status and microbial distribution and diversity of streams were assessed for a period of two years. Diversity indices revealed a decline in terms of microbial abundance and composition. Clustering and ordination analysis clearly separated reference site from coal mine affected sites. Low dissolved oxygen, low pH, high sulphate, iron are some characteristics of coal mine impacted sites. These patterns are the result of a combination of rampant dumping of untreated wastes exacerbated by geologic, topographic, climatic and land use factors.