A two-dimensional numerical model employing a fully transformed σ-coordinate system in the vertical direction is developed to analyze the scalar transport in an estuary. For a preliminary step of developing the numerical model, the influence of a coordinate transformation on the accuracy of the numerical simulation is investigated by comparing the computational results in both z- and σ-coordinates with analytical solutions. In addition, the numerical errors due to the transformation are investigated according as whether the diffusion term is fully derived or not. The numerical accuracy attributable to the full transformation is examined by comparing predicted results with those of the model employing only the partial transformation in a simply sloped topography. Finally, the numerical model developed in this study is applied to the Keum River estuary in Korea, for a salinity intrusion simulation. The calculated results showed good agreement with the observed field data, both of which clearly indicate that the tidal effect on the salinity intrusion are clearly discerned in the estuary.