This study provides an assessment of possible changes in the general circulation and residence time in the Persian Gulf under potential future sea-level rise and changes in the wind field due to the climate change. To determine the climate-change-induced impacts, Mike 3 Flow Model FM was used to simulate hydrodynamic and transport processes in the Persian Gulf in both historical (1998–2014) and future periods (2081–2100). Historical simulation was driven by ERA-Interim data. A statistical approach was employed to modify the values and directions of the future wind field obtained from the Representative Concentration Pathway 4.5 and 8.5 (RCP4.5 and RCP8.5, respectively) scenarios derived from CMCC-CM model of the fifth phase of the Coupled Model Intercomparison Project (CMIP5). The numerical model was calibrated and validated using measured data. Results indicated that in the historical period, residence time ranged between values of less than a month in the Strait of Hormuz and 10 years in the semi-enclosed area close to the south of Bahrain. The changes in wind field based on RCP 8.5 scenario were found to be the most disadvantageous for the Persian Gulf's capacity to flush dissolved pollutants out. Under this scenario, residence time would be 17% longer than that of historical one. This is mainly because the change in the wind field is large enough to overwhelm general circulation, showing a relationship between the residence time and the residual circulation. Impact of change in the wind field according to RCP 4.5 scenario on the modeled residence time is negligible. The numerical outputs also showed that the sea-level rise would slightly decrease the current velocity, resulting in a negligible increase in residence time. The findings of this study are intended to support establishing climate-adaptation management plans for coastal zones of the studied area in line with sustainable development goals.