Abstract: Based on the long term hydrological and bathymetric analysis, the morphological evolution in the estuary features the significantly large riverbed change, that is, the great erosion in runoff-dominated periods and the great sedimentation in tide-dominated period in the upper reach of the Qiangtang River estuary. This morphdynamic characteristics results in the large variation of tide in the upstream section and therefore affects saltwater intrusion. With plentiful runoff during wet seasons, the riverbed suffers great erosion, leading to the increase of river convey volume and enhancement of tide. This results in the increase of saltwater intrusion in falls with strong tide. On the contrary, with small runoff during wet seasons, the river convey volume is small. Therefore, it results in weakening saltwater intrusion in falls. The results indicated that the runoff variation has direct and indirect impacts on saltwater intrusion in the Qiantang River estuary. The direct impacts are the common characteristics of tidal estuary, i.e. saltwater intrusion increases as runoff decreases. The indirect impact is that the large erosion caused by the large runoff results in the increase of tide, and therefore indirectly leading to intensified saltwater intrusion. This feature results from the characteristics of the large riverbed change and its great response of tide strength in the Qiantang River estuary.