The circulation pattern is one of important factors for residence time of nutrients and pollutants in waters and river run-off has great effects on coastal and estuarine eco-system. The effects of river runoff on near shore circulation pattern are undertaken with FVCOM over a very complex topography with daily-averaged discharge data. The scope and strength of the river run-off under different discharge are discussed both for surface and bottom layers. The net surface circulation pattern of river is constrained by topography in narrow and coastal areas and affected by other factors in open sea. The net bottom circulation is weaker and in opposite direction to that of surface's in most waters. The river run-off has a delay and baroclinic effect on the circulation pattern.