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• Combined numerical model and GOCI to improve the ability of sediment flux (SF) estimation. • Multi-timescale SFs at typical cross-sections in YRE are estimated in 2013 and 2015. • Locally morphological changes are further estimated, showing erosions in 2013 and 2015. Sediment flux (SF) in the estuary is vital to the coastal and estuarine environment, especially the morphodynamical and ecological processes. However, its quantitative estimation with high accuracy is difficult because it is controlled by complex mechanisms and multiple processes. This study corrects the seasonal variations of the simulated suspended sediment concentration (SSC) by using GOCI-derived surface SSC and calculates the variations of SFs at the main cross-sections in and out of the Yangtze River Estuary (YRE). The results show that in 2013, 159 Mt and 143 Mt of sediments passed through Xuliujing hydrological station in YRE and estuarine mouth section, respectively. In the inner estuary, the significant seasonal variations of sediment transport are noted that the most seaward transport happens in summer (43.8%) and the least occurs in winter (7.3%). In the outer estuary, the southward transport towards Hangzhou Bay is the most critical pathway, accounting for 109.0% of total transport at mouth section, and is prevalent in autumn and winter. With considerations of sand mining and land reclamation, obviously erosions appear in the whole estuary during both 2013 and 2015. With stronger wind conditions in 2013, severer erosion (161 Mt) happens in outer estuary than that in 2015 (86 Mt). By combining the GOCI-derived surface SSC and the numerical model results, this study can better represent high-frequency hydro- and sediment-dynamical processes to calculate the annual, seasonal, and vertical SFs with improved accuracy. Hence this method may provide a viable way to infer locally averaged morphological changes. [ABSTRACT FROM AUTHOR]