Geostrophic transport can affect the structure of the wind-driven coastal upwelling/downwelling. Focusing on quantifying this impact is vital to understanding circulation dynamics in the Persian Gulf. To this end, in this study, after the investigation of wind patterns, the temporal and spatial structure of coastal upwelling/downwelling using the Ekman transport upwelling index, and the intra-annual vertical variability of temperature are investigated based on the daily wind, and monthly temperature data time series of 28 years (1993–2020). Then, the geostrophic transport using an improved methodology and the total cross-shore transport as a sum of Ekman and geostrophic transport are estimated based on the monthly SLA data time series. The results indicated that the region, located around 51.5 and 28 (48 and 29 and 50.5 and 25.5) experienced the most intense coastal upwelling (downwelling) at a peak in June with larger mixed and thermocline layers than other regions. The intensity of Ekman transport is higher than the geostrophic transport in the Persian Gulf due to the presence of the prevailing wind and the shallowness of the mixed layers’ depth. We found that the intensity of the coastal upwelling (downwelling) decreases (increases) under favorable spatial and temporal conditions by considering the geostrophic transport in the upwelling index.