This study aims at the long-term numerical simulations of the offshore region, the estuary and the channels in Touchien and Fengshan Rivers. Finite element tide and flow model was used to simulate the influence of offshore tide, wind, wave on the surge at the estuary. In addition to simulate the erosion and deposit in the upstream regions of these two rivers, the explicit finite analytic model was also used to provide information on the flow and sediment condition for the CCHE2D-Coast model to simulate the morphological changes at the estuary. The CCHE2D-Coast model was used to simulate the estuarine morphological changes under design flood and monsoon, namely 100-year flood applied to Touchien River, 50-year flood applied to Fengshan River, 100-year storm surge, and three-month monsoon, for the present layout and six proposed plans. According to the simulation results, the best among sixed cases can be obtained, i.e., Case 4. The hydrological conditions for the three-year longterm simulation as the input boundary conditions are assumed to consist of three historical typhoons (Haitang (07/17/2005 22:00 – 07/18/2005 21:00), Matsa (08/04/2005 14:00 – 08/06/2005 23:00), and Talim (08/31/2005 12:00 – 09/01/2005 21:00)) and a three-month monsoon (from December 1, 2005 to February 28, 2006). The three-year hydrological conditions are repeated three times of the three storms and one monsoon for predicting the estuarine morphological changes at confluence of Touchien and Fengshan Rivers. By summarizing the numerical results of all the six cases for flood stages and bed changes, it is found that Case 4 can better prevent the left bend of the Touchien eatuary from being inundated; and the dredged Jiugang right channel can alleviate the downstream flood by diverting the upstream flood water directly down to the river mouth. The numerical results of bed changes also indicate that the bed changes in Case 4 are more stable in the estuary than other engineering plans. The overall bed changes show that the flood currents flush the upstream river sands to the downstream, which deposit in the river mouth and the offshore, and create the offshore bar around the fishery harbor breakwater dike. This periodical event-dependent morphodynamic processes is in agreement with the natural mechanism of the development of the river mouth. The seasonal changes of bed elevations under the assumed hydrological condition show several characteristics such as: (1) The storms always create significant bed changes than the monsoons; (2) The monsoons play a role of a recovery forcing to compensate the bed changes by the storms; (3) The variations of the bed changes tend to be less and less along with the increase of time; and (4) The long-term variations of water elevations, flows, and bed changes in the estuary indicate that the periodical seasonal events (i.e., storms and monsoons) are likely to lead to a relative stable bathymetry (the so-called dynamic equilibrium state).