A sediment removal system and method provides a versatile and controllable device for removing sediment from water in a focused manner that avoids generating unwanted turbidity. A suction pump draws water and sediment through a suction conduit and the injection of air into the suction conduit by air nozzles enables sediment to be removed from greater depths. The inclusion of water nozzles on an inlet opening enables hardened sediment to be dislodged such that it may be drawn into the suction conduit. A GPS receiver mounted to the suction conduit enables the location of the removal process to be tracked and a knife valve prevents backflow out of the suction conduit. The capturing of solid sediment by retention containers and the capturing of water containing suspended sediment by a tank enables the sediment and water to be transported to an appropriate location for treatment or disposal.