The invention discloses a device for treating river water polluted by mercury. The device comprises an activated sludge adding device, a magnetic field generation device and an intelligent controller. The activated sludge adding device comprises a water pump, an activated sludge acclimation tank and an activated sludge discharging pipe. One end of the water pump is connected with the activated sludge acclimation tank while the other end of the water pump is connected with the activated sludge discharging pipe, and transgenic escherichia coli are cultured in the activated sludge acclimation tank. The magnetic field generation device comprises a magnetic field tester, a power supply, a transformer, iron cores and spiral coils, the spiral coils are peripherally wound on the iron cores and connected with the transformer which is connected with the power supply, a sensing end of the magnetic field tester is arranged in river water, the other end of the magnetic field tester is connected with the intelligent controller, and the spiral coils are arranged on two sides and at the bottom of the river water. The device is simple in structure, biochemical reaction and biomagnetic effects simultaneously occur in a river channel after a weak variation magnetic field is applied to microorganisms in a sludge area of the river channel, and accordingly selenium adsorption and degradation capacity of the microorganisms is improved, and addition of other chemical agents is avoided.