The climatic change has led to the sea-level rise (SLR), which is expected to continue based on the current industrial and human activities. Previous studies indicated that most of estuaries which are of great environmental and economic importance are likely to be affected by SLR. Thus, understanding the hydrodynamic behavior of estuaries under SLR is necessary. This study focuses on the Hudson–Raritan Estuary (HRE) which has been predicted to undergo relatively high SLR rates. The complex geometry of HRE including bays connected by tidal straits along with the multi-tidal inlets necessitates more investigation of the complex hydrodynamics in this region. Here, we studied the potential effect of the projected SLR scenarios to the year 2100 on salinity distribution and transport processes during the dry and wet seasons using the three-dimensional hydrodynamic model (EFDC). The model is validated by the field observations of water level, current velocity, salinity, and temperature distribution in the estuary. A comprehensive analysis of the current sea level (base) and the three projected scenarios of 0.35, 0.55, and 1.05 m rise revealed an increase of the average salt content and the stratification intensity as the water level rises in tributaries, with higher increase rates during the wet season. In addition, the results showed that the water exchange between different regions through tidal straits enhances under SLR scenarios. Furthermore, it was found that SLR amplifies the residual flows in tributaries and suppresses it along Ambrose and Raritan Bay Channels. Finally, our results showed that under SLR, the residence time increases in the tributaries due to changes in estuarine circulation. Conversely, the residence time decreases slightly in downstream of the estuary because of vertical mixing enhancement induced by decrease in stratification. The results provide beneficial information for understanding the response of transport process and circulation to SLR in the Hudson–Raritan Estuary.