The seasonal variation of water column is investigated by analyzing the observed temperature and salinity in the Yangtze Estuary. It is found that: the temperature stratification comes into being in spring along with the increase of the solar radiation; it becomes enhanced in summer and weakens in autumn, respectively; it vanishes in winter due to the strong vertical mixing mechanism as well as the decrease of solar radiation. On the other hand, the salinity distribution is affected by the runoff of Yangtze River. Therefore, the salinity stratification is the most obvious in summer and autumn, and it is not that apparent in spring. In winter, the northeaster prevails, and the Yangtze diluted water is confined to the coast, so the salinity is well mixed in the vertical. Furthermore, the dynamic mechanisms governing the seasonal variation of the water column are discussed. The above knowledge is essential for better understanding the distribution and transport of main nutrients and pollutants in the Yangtze Estuary.