An underground water channel is provided in an underground of a large depth, and rain water and the like flow into this underground channel from flood control channels, conduits and rivers through vertical shafts. A pump well of a pump station is connected to a downstream end of the underground channel, and water flowing into the pump well is discharged by a pump to a discharge tank. The pump is disposed generally at a medium water level of the underground channel, and a lowest water level L.W.L enabling draining is the medium water level of the underground channel. In an open channel flow operation of an open channel-closed channel mixed flow operation, water level of the underground channel is maintained at the lowest water level L.W.L, so that the underground channel is in an open channel condition. In the closed channel flow operation, the underground channel is fully filled with water, and further water level rises into the vertical shafts, so that the underground channel is in a closed channel condition. By changing an outflow factor in accordance with rainfall patterns, the rate of flow into the vertical shafts can be accurately estimated, so that the large-depth underground drainage facility can be run in a stable manner.