This paper presents a waterflow sensor for marine biologging. Although biologging methods have attracted attention in evaluating marine animals’ swimming performance, it has been difficult to directly measure the long-term waterflow velocity against a swimming animal. This is because the sensors require strict specifications, such as sufficient sensitivity and accuracy, small size and light weight, ability to move between water and air for breathing, and sufficient water pressure resistance. Here, we propose a waterflow sensor based on a closed-inlet Pitot-static tube structure that satisfies these requirements. The tube is filled with incompressible liquid. Silicone membranes are attached to the inlets to prevent air bubble infiltration. A differential pressure sensor chip, which works as the Pitot-static tube’s sensing element, is built into the tube housing to measure the pressure difference between the inlets. Due to the fluid incompressibility, the required pressure resistance is realized. The developed sensor responded to waterflow from 0.2 m/s to 1.6 m/s with sufficiently high sensitivity. Therefore, the proposed sensor can be utilized for the biologging of marine animals.