Two estuary and two coastal lagoon stations along Chennai, Southeast coast of India were monitored for 1. year to study both physicochemical and microbiological properties of the water. Influence of the marine environment over the systems was evident by elevated salinity levels. Considerable concentrations of total heterotrophic bacterial count and fecal bacteria such as total coliforms, fecal coliforms and fecal streptococci were observed throughout the study period which evinced a pattern of anthropogenic activities. Principle component analysis was employed for assessing the overall pattern of variation within the data sets. Climatic variation was highly correlated with changes in water quality, i.e. the Northeast monsoon and Summer had influenced considerably the microbial occurrence as well as the physicochemical parameters such as total suspended solids, chloride, sulphate and salinity. However, the effect of the Southwest monsoon was less prominent than the Northeast monsoon with its heavy rains. As both estuaries revealed elevated concentrations of polluted water, these stations can be used as indicators or alerts for the water quality along the coastal zone of Chennai. © 2013 Elsevier Ltd.