Multivariate statistical techniques involving factor analysis (FA) and dendrograms for hierarchical cluster analysis (HCA) were performed on nine water samples from Ennore Creek, Chennai, Tamil Nadu to assess the spatial distribution of water quality in each of three seasons. The water samples were analyzed for distribution of physicochemical parameters such as WT, pH, Salinity, DO, BOD, TSS, NO2-, NO3-, NH4+, TN, IP and TP. Results of factor analysis clearly indicates that factor 1 is dominant in monsoon season, since the estuarine mouth is partially opened (50-75m wide). When compared to pre and post-monsoon, maximum enrichment of nutrients occurs during the monsoon season. It is attributed due to the constricted outlet of the creek and large scale inflow of pollutants due to precipitation. Further the factor analysis indicates that the parameters responsible for water quality variations are mainly related to the influence of municipal sewage, agricultural effluents and industrial waste water. With HC analysis the water samples have classified into 3 clusters during the pre-monsoon season, monsoon season and post-monsoon season. pre-monsoon cluster II, monsoon cluster III and post-monsoon cluster III are having highest concentration in WT, BOD, NO3-, NH4+, TN, IP and TP. The characteristics and water quality of these cluster stations EBUCS, WQE4 and WQE5 are in direct relation with Buckingham canal source and NCTPS coolant water.