Water levels and flows in the Singapore coastal waters are driven by the complex interactions of the Indian and Pacific Ocean tides, seasonal monsoon-driven contributions and also forced by local winds. The Singapore Regional Model was developed to simulate hydrodynamics in the Strait of Singapore which produces representative sea level variation in this region. However, resolution and alignment of the grid system of the model with respect to depth contours in some of its subregions, i.e., the Johor Estuary area require further improvement. For this, the grid system of the model was modified and compared the simulated results with field measurements. The computed flow velocities agreed better with field observations when the grid resolution was increased. However, improving the alignment of the grid with the channel boundary (with a much lower increase in grid resolution) provided a substantially larger improvement of the model performance. The grid modification greatly influenced the computed salinity in the estuary, while water levels are slightly affected. Further analysis of model results showed a pronounced ebb tidal asymmetry generated by the O1–K1–M2 tidal constituents in the estuary.