Changes in temperature and salinity distribution in relation to depth and distance in the shallow Gosthani Estuary were studied during the four different seasons (December 1987 to 1988). The influence of gravity –impelled flow of freshwater from the head of the estuary and the vertical stratification in temperature and salinity that ensued were described. The effects of annually forming sand bar that occludes the mouth and the breaching of it later, and on the changing pattern of the temperature and salinity in estuary were considered in some detail. The effect of increased tidal inputs from the marine end marking the commencement of the recovery phase of the system from freshwater flooding and the establishment of horizontal and vertical gradients in temperature and salinity, was followed. The period of marine domination, when vertically isothermal and isohaline conditions prevailed, was a prolonged one.