Based on the hydrologic data of the Yangtze estuary 12.5 m deepwater channel in the flood season and dry season, we analyze the spatial and temporal distribution of suspended sediment concentration. The result reveals that suspended sediment concentration in the south channel & Yuanyuansha and the middle section of the north passage is small, and its vertical distribution is relatively uniform. But in the middle section of the north passage, the suspended sediment concentration is high and the vertical distribution is uneven. Fine sediment flocculation, fresh and salt water mixing and stagnation point may be the main reasons for the high suspended sediment concentration in the bottom of the middle section of the north passage and large differences in the vertical distribution of the flood season. The high suspended sediment concentration in the middle section of the north passage and in the flood season is consistent with the characteristic of temporal and spatial change of 12.5 m deepwater channel siltation, indicating that siltation in the north passage resulting from the suspended sediment’s deposition. The suspended sediment concentration in the south channel & Yuanyuansha is significantly lower than that in the north channel, and the vertical distribution is relatively uniform, which indicates that the contribution of channel siltation from suspended sediment silting may be small.