The Yangtze River is not only the largest river in China, but also the most important water transportation artery. Some parts of the river, however, still have barricades formed from sunken ships emplaced during the Anti-Japanese War on the Chinese mainland (World War II) to interfere with shipping. The Madang section, with its shallow water depth and the blockage in the channel, has raised safety concerns for transportation on the Yangtze River. This paper discusses the detection of sunken ships on the Madang section using a geophysical technique and describes general procedures for conducting high precision magnetic surveys on water. It also introduces an approach for recognizing the interference caused by nearby moving boats. Finally, it discusses the techniques used to accurately determine the position and quantity of ships buried at the bottom of the river from the magnetic data. The seven sunken ships that were identified from the magnetic data in this survey area were raised in a subsequent salvage operation. The positions and dimensions of the sunken ships deduced from magnetic data coincide with the locations and sizes reported by divers. For example, the estimated length of the ship associated with anomaly M4 is 84 m in length, and the actual length measured by divers in water is 85 m. No other sunken ships have been found by the transportation company in charge of the salvage operation subsequent to the removal of the seven sunken ships mentioned above. This indicates that a magnetic survey is the most effective technique to detect submerged ships.