The prediction of pollutant transport in natural water bodies is becoming an essential task. The water quality prediction models basically simulate the physical process and their performance relies on the estimation of parameters such as vertical eddy diffusivity. An aim of this study was to compare the performance of different methods of estimation of the vertical eddy diffusivity in a coastal water body. The field study was carried out in the Swan River Estuary, Australia. The turbulent properties were measured by using a microstructure probe. Field measurements indicated that the different methods might result in different estimation of the vertical eddy diffusivity. Therefore, these traditional methods which are successful in some cases in the ocean, can not be used in all estuaries.