The invention discloses a treatment system and a treatment process for removing polluted bottom mud of lakes, reservoirs and riverways. The treatment system comprises water body isolation equipment, slurry stirring equipment, centrifugal dewatering equipment and sludge storage and transportation equipment, wherein the water body isolation equipment, the slurry stirring equipment, the centrifugal dewatering equipment and the sludge storage and transportation equipment are communicated through pipelines, the water body isolation equipment comprises a plurality of isolation cavities capable of being spliced with one another and a crane for lifting and aligning the isolation cavities, the centrifugal dewatering equipment comprises a sludge conditioning and stirring system, a sludge-water separation system, a sludge dewatering system and a sludge cake spiral conveying and unloading system, the sludge storage and transportation equipment comprises a storage and transportation ship body, positioning piles for supporting the storage and transportation ship body and a mud bin located in the storage and transportation ship body, and a spiral discharging machine is arranged in the mud bin. According to the invention, the movable treatment station is adopted, all devices are arranged on a ship for operation, land resources are not occupied, the treatment method is simple, bottom mud and water body are directly separated, mud-water separation is implemented in real time, and the water content of dry mud is as low as 60%.