Understanding the source and type of pollutants during the flood events of a stream play a key role in decision making for estimating and controlling river pollution. During high floods, the non-source pollutants get washed through the drains and then enter the main stream. This brings a high anxiety over stream water quality improvement and regulatory decision. Soil and Water Assessment Tool (SWAT) is one among the techniques for deterministic, continuous, watershed-modelling to the pollutographs and load graphs, thereby, estimating the ecological changes in a water stream. SWAT modelling gives definitive idea about the pollutant and flow characteristics to optimally and effectively manage existing drains to bring the pollutants concentration to minimal amount during high flood conditions. A sub-basin of Thamirabarani region, with an area of about 10.18km2, is analyzed for pollutant concentration from 2016 to 2017, to identify and rectify the sub-basin with maximum pollutants and the reasons for the same. In this study it was found that, the amount of N and P pollutants depends on the vegetation cover, land parcel changes, areal extent of precipitation, built up area and semi-arid region corresponds to discharge of sediments to main stream. © 2017 IAEME Publication.