Fish locomotor performance depends on inter-individual morphological differences and influences the response of populations to anthropogenic impacts. Amphidromous gobies, Sicyopterus lagocephalus and Cotylopus acutipinnis can climb up obstacles several metres high, after their arrival in rivers from the ocean. A previous study demonstrated that juveniles of S. lagocephalus performed better than C. acutipinnis when challenged with an artificial climbing ramp, and that individual morphology explained climbing performance for both species. This present study was focused on the effects of two 10-m high dams on the individual morphological selection of these species. We hypothesized that, compared with C. acutipinnis, (a) S. lagocephalus juveniles will reach the dams faster after they arrive in freshwater and (b) their morphology will play a lesser role in their capacity to climb up the dams. Anatomical traits were measured for 186 and 201 S. lagocephalus and 179 and 221 C. acutipinnis captured downstream and upstream of the dams, respectively. The time they spent in freshwater was estimated by examining the microstructures of their otoliths. As expected, S. lagocephalus individuals reached the dams 10–20 days faster than C. acutipinnis, and their morphology upstream and downstream of the dams did not differ, in contrast to C. acutipinnis. Upstream of the dam, C. acutipinnis had a larger pelvic sucker than downstream, confirming experimental observations. It suggests that juveniles of the cosmopolitan S. lagocephalus have more efficient upstream migration capacities than the endemic C. acutipinnis. Moreover, differences in individual morphologies above and below barriers appear efficient for quantifying their impact on upstream migration of amphidromous species.