Intensive anthropogenic impacts have been implemented in the Yangtze estuary during the last several decades, which significantly modified the global and local hydro- and morpho-dynamics. Subsequently, sediment movement characteristics in the vicinity of the Deepwater Navigation Channel (DNC) change in accordance with such human interactions. The present study is focusing on the recent sediment moving features around the DNC in between 2017 and 2019, after the elevation of the partition dike in 2016. Five successive in-situ regular campaigns for flood and dry seasons, together with field surveys pre- and post-typhoon in 2018, were conducted to collect bottom surface sediment samples. Sand and silt samples with different physical properties were identified. Under the normal weather condition, sand samples are generally found in the South Channel (SC) and the middle reach of the North Passage (NP), whereas silt samples are prevailed elsewhere. Considering the different features in the grain size distribution curve of sand samples, more attentions were paid to the spatiotemporal variations of sand samples. Grain size parameters of sand samples indicate that under the normal weather condition, relatively pure sands with almost no silt constituent exist in the SC, whereas relatively mixed sands with certain silt compositions are located in the middle reach of NP. Nevertheless, only relatively mixed sands could be found in the SC and there are no sand samples in the NP after typhoon events. Subsequently, the recent sediment movement characteristics in the vicinity of DNC were figured out. Under the normal weather condition, relatively mild siltation owing to the back-filings from the dike fields and seaward of DNC occurs in the middle and lower reaches of DNC, which is consistent with the temporal variations of the magnetism analysis of sand samples. In contrast, intensive siltation occurs inside the DNC after the extreme weather events, which comes from three possible provenances, i.e., overtopping from the south dike, back-fillings from dike fields and seaward of DNC. These findings provide some helpful information for the efficient management and reasonable regulation in the Yangtze estuary.