This study designed and demonstrated a two-dimensional multi-inlet waterflow sensor to address challenges associated with measuring the swimming speeds of marine animals owing to size limits and harsh marine environmental conditions, such as clogging by marine debris. The sensor comprises a spherical housing equipped with three pairs of inlets on opposite sides, each connected to a differential pressure sensor element through a tube filled with an incompressible liquid. Notably, a sealed film placed over each inlet prevents marine debris from intruding into the sensor. The differential pressure data collected by the three sensor elements are used to determine two-dimensional waterflow speed and angle using a neural network trained on water tunnel experiments. The results of the experiments conducted in this study demonstrated that the developed sensor can accurately detect the waterflow speed and angle within a speed range of 0.6–2.0 m/s, which is typical of green turtles. Therefore, the proposed sensor is expected to realize improved biologging of marine animal behaviors.