It was observed that the extremely low discharges of the Changjiang River, caused by a serious drought in the river’s basin in summer 2006, made a strong saltwater spring over the North Branch in the Changjiang Estuary occured in that year 3 months earlier than usual. The salinity at surface was higher than the one at bottom in the South Branch near the bifurcation of the South and North branches, vertical stratification was obvious, whereas the salinity was vertical homogeneous in the other place of the South Branch due to the strong vertical tidal mixing. Due to the effect of saltwater spilling over from the North Branch into the South Branch and salinity accumulation, the occurred time of the maximum salinity at the Chongtou was about 3 days later than that of the highest tidal level at Qinglonggang, and it took about 2 days for the spilling over saltwater to the downstream Chenhang reservoir by the river discharge.