Singapore’s coastal waters are characterised by relatively complex tidal behaviour due to it’s location between two large oceans with different tidal regimes. This complex tidal behaviour results in poor understanding of the hydrodynamics and sediment dynamics. The hydrodynamics of the Johor River estuary, including part of the Singapore Strait and the Johor Strait, are investigated with a computational model in order to enhance the understanding of the sediment dynamics. The computational model used for this study is the Singapore Regional Model Refined and Aligned (SRMRA), which was developed applying the Delft3D modelling system. The domain of this validated model covers part of the Andaman Sea, South China Sea and Java Sea. An intra-tidal analysis over a period of 25 hours reveals that the tide propagates throughout the entire study domain up to the northernmost part of the Johor River. During the ebb phase in the estuary, the flow in the Singapore Strait is in the eastern direction. In contrast to many other shallow estuaries, the water levels are observed to be ebb dominant the further upstream. The transport patterns in the Johor River estuary on a larger timescale are described by means of the residual flow. The depth averaged residual flow is stronger and more multi-directional near the mouth of the Johor River estuary than in the upstream part. An ebb dominant and flood dominant channel can be observed. The residual flow in the surface layer is directed in the ebb direction and the residual flow in the third layer from the bed is directed in the flood direction. Moreover, the residual flow in the surface layer is stronger than the residual flow in the lower layer. The model predicts roughly a larger bed shear stress in the southern part of the Johor River estuary than in the northern part. In the area around Pulau Tekong the bed shear stress consequently was found to exceed most of the time 0.1 N/m2, which is considered a reasonable value for the critical bed shear stress for erosion of fine sediments. In the northernmost part of the Johor River the predicted bed shear stress is small enough for a sediment trap to be developed. Analysis of the particle paths shows that during the period of flood tide, flow from the Johor Strait may travel into the Johor River. Once a particle flows out of the estuary into the Singapore Strait during ebb, it is not likely to flow back into the estuary during flooding.These findings contribute to a larger understanding of the hydrodynamics and sediment dynamics of the Johor River estuary.