A simulation of water level, velocity, salinity, and temperature in the Bay of Benoa has been carried out using a three-dimensional hydrodynamic Estuarine and Coastal Ocean Model incorporating a main characteristic of southward transport of the Indonesian throughflow at the offshore area of the bay. In other respects, two types of boundary conditions have been tested: (1) specifying elevation at all boundaries; and (2) implementing a combination of elevation and velocity at the boundaries. Performance of the model results has been quantified in terms of mean absolute errors, root-mean square errors, and correlation coefficients based on the availability of water level and current data. The general agreement between simulated and observed values of water elevation and currents is encouraging. Errors in computed water levels are less than 5 % of the local tidal range, and correlations between the data and model exceed 0.95. Meanwhile, errors and correlations for simulated currents are less than 22 % and are about 0.75, respectively.