The Nagaon Paper Mill(NPM) discharges their heavily loaded waste effluents @2100 m3/h into the natural wetland system called Elenga Beel located in Morigaon district of Assam(India).Due to higher chemical diversity of Paper Mill Effluents (PME) it impairs with the water quality as well as endangers aquatic life . The effluent altered physico-chemical and biological nature of receiving water body in a number of ways. Among aquatic organisms algae are the first hand indicators and very sensitive to pollutants. Any change in their environment may leads to change in algal communities in terms of tolerance, abundance, diversity and dominance in their habitat. To prove this hypothesis the present study was undertaken.