Of all the factors involved with sound propagation in very shallow water, the water temperature has the greatest effect on the sound velocity. However, there are considerable difficulties in measuring the water temperature in the sea. Therefore, we propose to install a thermister chain in a commercially available remote-control boat with sounding capability. First, we conducted an experiment to compare the measuring function between the remote-control boat and other reference equipment to survey the accuracy of our proposed method. The results confirmed the accuracy of position, sounding, and temperature measurements made by the boat in practical use. Next, we measured water temperature profiles in Hashirimizu port using the remote-control boat system. According to the temperature data, unexpected changes of water temperature were found at different locations and times, caused, we believe, by variations in the air temperature accompanying weather conditions. Finally, we calculated the sound ray trace using actual sea temperature data and confirmed the available path for sound propagation in very shallow water.