Numerical method of discontinuous Galerkin (DG) discretization for coastal ocean modelling have advanced significantly, but there are still challenges in accurately simulating phenomena such as wetting and drying process and baroclinic flows in coastal and estuarine regions. This study develops a novel 3D coastal and estuarine modelling system, DGCEMS, using a quadrature-free nodal DG method. The model adopts <em>σ</em>-coordinates, employs a non-split mode framework, and integrates a semi-implicit Runge–Kutta scheme with second-order accuracy in both space and time. A series of numerical experiments demonstrate the model’s second-order convergence, low spurious mixing, and capability to simulate salt-freshwater interactions in the presence of wetting and drying boundaries.