We constructed a portable target strength measuring system for small targets like zooplankton. An acrylic water tank (60×60×180 cm) was used for the experiment. This was a bistatic system using two transducers at 400 kHz. The target strength of two cylinders was measured and compared with a sound scattering model to confirm that the system could measure target strength exactly. The model predictions were compared to measurements, and we confirmed that precise measurements of target strength were possible. In addition, we measured the side-aspect target strength patterns of Euphausia pacifica, which inhabit many of the ocean areas around Hokkaido. We confirmed that measurement was possible in an area with a noise level of approximately −90 dB.