A smart dredging system for polluted sediment in a river, lake, or estuary, comprising: excavation equipment (10), used for dredging a river, lake, or estuary and extracting polluted sediment; pipeline transport equipment (20) comprising a transport pipeline (22) hermetically connected to a sludge discharge pipe (12) and used for discharging the polluted sediment outputted by the sludge discharging pipe (12), where the sludge discharging pipe (12) and the transport pipeline (22) are sealed throughout.