Kolkata city sewage purification process is rapid, extremely efficient and the process is operated in single pond systems at East Kolkata Wetland (EKW) in a highly sustainable manner. However, the underlying mechanism remains unclear. Since microbial activity plays vital role in wastewater purification, an understanding of the microbial community structure and their functions during purification is crucial. Therefore, we investigated the microbial community structure at different phases of this purification process. To unveil the microbial community structure, we performed 16S rDNA-based community analysis. The microbial community was found to be composed of methane producing, sulphate reducing, ammonia oxidising, nitrifying, denitrifying, phosphorus accumulating and other types of microorganisms. Results also showed that microbes with versatile metabolic potential grow at different phases of purification process and the microbial diversity and complexity decreases considerably with the progression of purification. Beside this, studies on the distribution of microbial population reveals that the community achieves more stability at later phases of purification. Thus, the current study documents the variations in microbial community structure during wastewater purification in single pond unit at EKW and provides an insight into the underlying mechanism of this type of unique process.