Abstract In this study, the Navier-Stokes equations that embrace conservation equations of momentum, volume, heat and salt are solved by using a 3-D numerical model. Then, based on the values obtained, the structure and variability of the outflow/inflow between the Persian Gulf and the Gulf of Oman is investigated. The basic equations are cast in a bottom-following, sigma coordinate system which greatly simplifies the numerical solution. Conservative finite difference methods are used to discretise the mathematical model in space. The model results, which are in agreement with limited direct measurements in the Strait, show a volume transport of deep outflow and a near-surface outflow from the Persian Gulf to the Gulf of Oman through the southern part of the Strait. About 65% of total outflow occurs in the bottom layer (40 m to the bottom) and 35% in the upper layer (from the surface to 40 m deep) during the year. The annual mean of surface inflow from the Gulf of Oman to the Persian Gulf, which occurs within the northern part of the Strait is about 0.2 Sv. The net volume transport annual mean through the Strait into the Persian Gulf is about 0.03 Sv. Strong temperature and density contrasts between bottom and surface layer waters are established in spring and summer. These are more pronounced in the southern part of the Strait. In the northern part of the Strait, the salinity contrast is nearly constant, but in the southern half it varies significantly during the year.