## 1 Introduction
Tyhoons or hurricanes are the most energetic atmospheric force acting on coastal and estuarine waters, which certainly cause significant changes in water level, dynamics and mixing [28; 29; 30; 31]. For many years, the study of storm surges has been largely focused on the extreme water level variations. Observations and numerical simulations have indicated a strong salinity variation during hurricanes and storm surges induced by cyclones [32; 33]. From a post-disaster survey, [PERSON] et al. [34] reported that higher water levels in the inundated area, or runup heights, were found on the coast facing north due to the super typhoon, Meranti, which migrated toward the WWN direction. [PERSON] et al. [35] studied two opposite dynamic effects (east-path and west-path typhoons) on saltwater transport and stratification in the Modaomen waterway of the Pearl River Estuary, and discovered that the east-path typhoon led to the set-down of the coastal sea level, and increased the oceanward advective flux, while the west-path typhoon resulted in the set-up of the coastal sea level, which promoted the landward advective flux and caused more serious saltwater intrusion. [PERSON] et al. [36] investigated two cases of different hurricanes and concluded that the stronger wind force clearly altered the pattern of salinity intrusion. Besides, salinity stratification is also an important phenomenon in the estuary as illustrated by [PERSON]'s kinematic estuarine salt balance, stratification determines the volume transport of oceanic water into an estuary. Both observations and modelling work testified to the stratification change induced by storm events in many estuaries [37; 38; 39], but the typhoon-induced salinity intrusion and horizonal distribution were rarely popular topics when comparing larger estuaries. The Yangtze River is the longest river in China, with a length of 6380 km, spanning 19 provinces and with a catchment area of 1.8 \(\times\) 10\({}^{6}\) km\({}^{2}\). The Yangtze River Delta is one of the most developed economic areas in China. The YRE (Figure 1) is divided into the NB and the South Branch (SB) by the Chongming Island, while the Changxing Island and Hengsha Island divide the lower SB into the North Channel (NC) and the South Channel (SC). Finally, the lower SC is divided into the North Passage (NP) and the South Passage (SP). The YRE has a complicated topography with third-order bifurcations and four outlets into the East China Sea, and the salinity intrusion can significantly impact the four large-size drinking-water reservoirs that supply drinking water to about 50 million people. Many studies investigated the YRE: its plume characteristics [40; 41], impacts of river discharge [42; 43], SLR [44; 45] and Three Gorges Reservoir [46; 47]. However, little information, which focused on coastal inundation [48] and dynamical responses of river plumes [49], is available about the influence of short-lived episodic events such as storms and typhoons, which may significantly influence the vertical mixing processes. The NB is the first bifurcation; it has the lowest river discharge in the four branches and is mainly dominated by tidal force, which is vulnerable to typhoons. In this study, we aim to investigate responses of hydrodynamics and saline water intrusion in the NB of the YRE to Typhoon Fongwong, which landed in Shanghai, using a process-based numerical model based on MIKE3. Firstly, a three-dimensional hydrodynamic and salinity transport numerical model, with a high-resolution unstructured mesh and spatially varying bottom roughness, was developed and validated quantitatively against hydrodynamic and salinity measurements. Secondly, the spatio-temporal hydrodynamic characteristics and salinity in the NB during Typhoon Fongwong were analyzed. Finally, we discussed the effects of the typhoon on hydrodynamics and salinity through the comparison with a scenario of normal wind force action.