Abstract: Investigations on physico-chemical parameters like temperature, pH, salinity, dissolved oxygen (DO), nitrate, nitrite, inorganic phosphate and silicate were carried out in two different zones of Vellar estuary, South east coast of India from Sep. 2006 to Aug. 2008. Nitrate, silicate and DO were relatively high in monsoonal months (Oct-Dec) than the non-monsoonal months. Salinity, pH, atmospheric and water temperatures showed their maximum in middle of summer (May) and onset of pre-monsoon (June), whereas their values were minimum in monsoon. Two way ANOVA indicates, spatial and temporal variation of salinity which showed significant differences, but the other parameters showed significant temporal variations only. Factor analysis revealed that three principal components (PCS) contribute 84.47% total variances in physico-chemical characteristics of Vellar estuary, in which the first component attributed to river run-off from agricultural lands, mangrove leaf litters from Pichavaram mangroves (55.98%), the second to influx of neritic water from Bay of Bengal (17.72%) and the third to anthropogenic activities (10.77%). Maximal influence on first factor in physico-chemical parameters was found during the monsoonal months, thereafter it’s influences were declined when the second factor make dominance into estuary. Third factor influences were found throughout year but their effects depends upon first two factors.