Conventional methods for surveying diadromous fish migration from marine coastal waters to freshwater habitats are mainly based on electrofishing, a non-optimal technique for the study of fish migrations in rivers, and fishermen catch data. Underwater video has been recognized for a long time as a good alternative, but those approaches usually require intensive labour for retrieving the information from the video sequences. To overcome these problems, an underwater video system specifically designed for field work (low-weight, low-cost and autonomous) named BichiCAM has been developed for automatically counting, measuring and tracking fish observed in video sequences. The efficiency and precision of the BichiCAM system were tested by filming Sicyopterus lagocephalus juveniles passing through the camera field of vision in the Saint-Etienne River, Reunion Island, Western Indian Ocean. The BichiCAM system accurately measured fish length of the observed individuals when lens distortion of the camera was corrected, and the error percentages on the measurements presented a standard deviation of 5.1% of the total length. The BichiCAM system provides a powerful tool that will not only facilitate research on migrating fishes and invertebrates' communities but also allow studies of the effectiveness of fishways associated to dams or the impacts of fishery activities.