East Kolkata Wetland (EKW), a Ramsar site, greatly contributes towards purification of city sewage employing single pond system. However, the underlying mechanism remains unknown. Therefore to gain an insight, in this study efforts have been made to understand the rate of biodegradation and the time dependent changes of different physicochemical factors and their interactions that are involved in the process. For this purpose, different parameters such as BOD, COD, faecal coliforms etc. have been measured at different time intervals during the purification process. The results reveal that biodegradation rate at EKW pond is very high and wastewater gets stabilized within 10 days of retention. The higher rate of biodegradation in pond system at EKW (k = 0.7 day−1) than in laboratory based in vitro experiment (k = 0.12 day−1) reveals the important contribution from other environmental components that are unique for this system. The results also demonstrate the significant influence (P ≤ 0.01) of temperature, pH and dissolved oxygen on the purification of waste water. Thus the current study provides an insight about the optimal pathway of gradual improvement of wastewater quality in the single pond system at EKW and may serve to explore the inherent mechanism to a great extent.