The coverage and variation of submerged macrophyte, which plays an important part in lake ecosystem, is a good indicator for assessing the water ecosystem of the Gonghu Bay. The submerged macrophyte coverage of the Gonghu Bay was investigated by DT-X split-beam sounder, and the results were compared with the analytical results of remote sensing. As for 1m and 10m transects coverage, there was little difference between the results of DT-X and quadrate investigation. The results show that it is easier, highly efficient and more accurate to use hydroacoustic method for submerged macrophyte coverage investigation.