Downstream migrating anguillid eels face many barriers including turbines and pumps at impoundments for water abstraction, power generation and water level control, when attempting to exit the freshwater catchment to reach spawning grounds. Multiple eel species worldwide are facing different levels of endangerment and alleviating the impacts of barriers to migration is essential to allow completion of the life cycle. Deep bypass systems with entrances located near the riverbed hold some promise for increased effectiveness compared to traditional downstream guidance and bypass facilities with entrances near the surface, as eels typically occupy the bottom of the water column. Here we evaluate two deep entrance bypass designs; an airlift (the Conte Airlift) and a conventional gravity siphon of the same entrance dimensions. Tests were performed using migratory silver-phase American eels (Anguilla rostrata), at night, in a simulated forebay environment. Passage performance was monitored over a 3 h test period using both PIT (passive integrated transponder) tag and video recording equipment. Entrance velocity was fixed at 1.2 m s⁻¹ in each of 8 test runs with cohort size fixed in six runs at 14 and in two runs at 42. Test eels readily located, entered and passed both bypass designs. Differences in performance metrics between the airlift and siphon were not statistically significant (P > 0.05) with linked mean values of 74.5%, 90.5% and 100%, respectively. Eel length did not affect passage speed (P > 0.05) or slip ratio, i.e., the measured eel velocity relative to fluid velocity. The slip ratio was, however, greater in the siphon than in the airlift (P < 0.01) within identical vertical upflow sections of the test equipment. Siphon slip ratios in the upflow vertical section were comparable to those established for the horizontal and downflow sections. Fish density did not affect attraction and passage through the airlift or siphon. No mortality or signs of injury were observed on any of the test eels through a 48 h post-test observation period. Both airlift and siphon downstream bypass systems show promise as effective technologies for protection of downstream migrating eels at a variety of water diversion or hydroelectric sites that pose threats of impingement, entrainment, and turbine mortality.