There are various techniques for identifying fish species, including the multi-frequency method, in situ target strength characteristics, and digital image processing methods. Acoustic Doppler current profilers (ADCPs) are able to determine multiple current fields simultaneously and have been used to observe the swimming speed and behavior patterns of shoals of pelagic fish under natural conditions. In this study, we evaluated a classification method that can be used to determine the swimming velocity of both the sound-scattering layer and pelagic fish shoals using an ADCP (153.6 kHz) and a scientific echosounder (38, 200 kHz). To calculate the actual swimming speed of the fish shoals, the mean swimming velocity vectors of each stratified bin must be compared with the mean surrounding three-dimensional (3D) current velocity vectors. We found the average 3D swimming velocity of the sound-scattering layer to be characterized by a deviation of >5.3 cm/s from the surrounding current field. The average 3D swimming velocity of Pacific saury Cololabis saira was calculated to be 91.3 cm/s, while that of lanternfish Diaphus theta was 28.1 cm/s. These swimming speeds correspond to 4.19- and 4.26-fold the body length, respectively. Thus, the use of ADCP swimming velocity data can be expected to be a valuable species identification method for various fishes distributed in a given survey area.