This study presents a waterflow sensor for biologging of marine animals. Although a biologging method of recording animal behavior with sensors is attracted attention for evaluating the swimming performance of marine animals, it is not easy to measure waterflow velocity for a long time. This is due to strict requirements such as compact size and high pressure resistance. In addition, marine animals move above the sea surface to breathe. Here, we proposed a compact Pitot-static-tube-based waterflow sensor for biologging of marine animals. Incompressible liquid is sealed inside the sensor housings to realize high-pressure resistance. A thin film is glued inlets of the sensor to prevent air bubbles invention. A membrane-type differential pressure sensor chip is built inside the sensor to measure differential pressure between each inlet. By downsizing the sensor shape and reducing sealed incompressible liquid, the sensor is compacter than a previous sensor. The developed sensor responded to waterflow velocity from 0.2 to1.6 m/s with sufficiently high sensitivity.