Physical, biological, and chemical approaches should be comprehensively taken to evaluate the environmental conditions of a sea area with tidal mud flats like the Ariake Sea. In this study, a quantitative echo sounder was used to develop an acoustic method for remote and planimetric on-board observation on the distribution of the sea water and the floating mud layer which contain toxic substances like hydrogen sulfide. Based on the acoustic data, accordingly, material balance in tidal mud flats and underwater environmental conditions were evaluated. Specifically, a correlation between underwater acoustic data and the amount of hydrogen sulfide was established based on the indexes of transducer frequency and echo sounder manufacturer.