To conduct engineering geological investigation in waters, common geophysical prospecting methods frequently fail to satisfactorily determine bedrock topography as well as strike and development extent of the blind fault in the investigated area. Taking the traversing project of the Yangtze River natural gas pipeline network in Jiangjin as a study case, the authors detected the river depth, overburden thickness and bedrock topography of the whole area by adopting the transient electromagnetic method to carry out survey in waters. Drilling verification shows that data consistency is fairly good, suggesting that the transient electromagnetic method has a good prospect in waters survey.