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A three-dimensional numerical model has been developed to simulate flow and tracer transport processes in disinfection contact tanks. For modelling of the water surface, the rigid lid approximation and a new method were both considered. The new method for water surface representation, connected a 2-D model for the top layer to a 3-D hydrodynamic pressure model for the lower layers. The advantage of this method, in comparison to previous 2-D and 3-D models, is that this new method uses a hydrostatic pressure assumption only in the top layer for calculations of water depth. The model was applied to laboratory model of Embsay contact tank, which is operated by Yorkshire Water in UK. There was generally very good agreement between the numerical predictions and laboratory data for both flow and tracer transport model.Various scenarios were simulated and the influence of the main model parameters on the predicted velocity distributions were examined. Finally, the model was used to study the effect of various baffle arrangements for the Embsay tank. The results showed that the tank efficiency was highly dependent upon the baffle structure.