The delta of the Mekong River is one of the largest in the world, with the Mekong River carrying a large amount of sediments in its Region of Freshwater Influence (ROFI). This study investigates the flow structure and movement of both suspended and bedload sediments in the ROFI of the Lower Mekong Delta (LMD) in order to identify areas prone to sediment accretion and erosion. This is accomplished by applying the three-dimensional Coastal and Regional Ocean COmmunity (CROCO) model and then calculating the sediment budget of different stretches of the coastline. The model outputs, depicting areas experiencing sediment accretion and erosion along the coastline of the LMD, are then compared against observations obtained during the period 1990–2015 and demonstrate the ability of the model to identify areas particularly prone to erosion and where preventive actions against coastal erosion should focus.