The invention relates to a running water pump station for treatment of a black and odorous water body, and belongs to the technical field of urban water environment. The running water pump station comprises a submersible pump, a protecting cover, a pump base plate, a reinforcing layer, a running water pipeline, a pipe bracket and a pipe plug; the protecting cover is of a stainless steel rectangular frame structure, the submersible pump is covered with the protecting cover, the protecting cover and the submersible pump are fixed to the pump base plate through bolts, the lower layer of the protecting cover is a closed thin steel plate, thus river bottom silt can be prevented from flowing in, a movable cover plate is arranged on the upper layer of the protecting cover, and thus later maintenance is facilitated; the pump base plate is located on the reinforcing layer and used for fixing an upper structure; and the running water pipeline is connected with the submersible pump and fixed to arevetment through the pipe bracket. According to the running water pump station, the running water pump station is mounted in a river way, the land is saved, meanwhile, river water is directly pumped, a control cabinet is arranged on the revetment, the running water pump station can be directly operated and controlled on the revetment, the structure is simple, operation and management are convenient, operation is stable, overall hoisting and maintenance are achieved, arrangement of water intake wells can be reduced, the engineering investment is reduced, and the running water pump station isespecially suitable for treatment of the black and odorous water body in an urban area with land shortage.