For obtaining the rules of seawater intrusion in the Modaomen Waterway of the Pearl River Estuary, almost half a month, the hydrology and salinity were synchronously measured at the river section from Zhuyin down to Koumen. The results show that the salinity in the Modaomen Waterway generally presents a decreasing trend from downstream to upstream. In Koumen, the average salinity in surface water and at bottom, under different tides and flood-ebb fluctuation, has a large difference with a variation range between 1.7% and 2.4％, whose layering is clearer in dry seasons. Additionally, the difference in ebb period is typically larger than tide rising period. However, in Zhuyin, the salinity in surface water and at bottom, under different tides, has a small difference, with the average salinity lower than 0.1％ under flood-ebb fluctuation. From the perspective of ratio statistics of differences between surface and bottom salinities along the Modaomen Waterway, the average salinity at bottom is 43.1％, 53.4％, and 77.4％ higher than that in surface water in spring, middle, and neap tides, respectively. Furthermore, there exits better corresponding relations between velocities and salinities along water depth, so it is easier for the emergence of gravity flow during the neap tide. Closely to Koumen, salinity linearly decreases with the decrease of water depth; in upstream, salinity demonstrates the index declining rule. In addition, termination points of the two distribution rules are respectively about 23 km under spring tide and 17 km under middle and neap tides far from Koumen.