Water seepage can cause serious problems in geotechnical engineering especially for construction under the water level. Baghdad metro tunnel is one of the leading vital projects to solve the major problem of crowding roadways in a highly population increase city like Baghdad. In this study, the seepage rate that will flow toward different selected points along the tunnel section across Tigris River was calculated during the excavation process, with the consideration of three different water levels of River at maximum, moderate, and minimum water depths. A three-dimensional model of the study has been modeled using the finite element software (PLAXIS 3D V20). The water seepage was observed for six different locations on each route of the tunnel. The study showed that the change of water depth in the river has no significant effect on the seepage – time curve shape. However, increasing the water level in River from minimum to maximum leads to increase the seepage rate about 15%.