The cumulative frequency of low tidal level of navigation is an important index for navigation channel design, improvement and benefit evaluation. Normally, the cumulative frequency could be calculated by the number of days that the water level is higher than the designed lowest navigable water level. In the Qiantang river estuary of Zhejiang Province, the bed erosion and deposition is drastic, and the low tidal level is closely related to the bed elevation changes. Hence the aforementioned method could not count definitely the cumulative frequency in Qiantang estuary. In this study, the historical bathymetries since 1980 were used to analyze the bed evolution patterns in the annual years at Qibao section in Qiantang estuary, and the relationships between the variations of low tidal level and the bed erosion/deposition were discussed. On this basis, a new method based on the actual water depth under daily low tidal level was proposed for the calculation of cumulative frequency. According to the hydrological characteristics of Qiantang estuary, three typical hydrological years representing high flow year, normal flow year and low flow year were chosen to analyze the cumulative frequency of water depth for navigation in Qibao section. The results show that in the three years, the cumulative frequencies at Qibao section could reach 100%, 100% and 87%, respectively, which agrees with the reality. This method could be also applicable to other tidal estuaries where changes of bed elevation and low tidal level are remarkable.