In 2012, the fishway in the Miyanaka Intake Dam in Niigata Prefecture, Japan, was reconstructed and divided into three fishways (ice‐harbor‐, stair‐, and rock‐ramp‐type) with different flow velocities and water depths. We conducted an adaptive monitoring survey in these fishways from 2012 to 2020, and 33 fish types were found, including migratory, swimming, small swimming, and benthic fishes. Many species displayed a preference for specific fishways. The run‐up for Tribolodon hakonensis was studied to determine the effects of physical parameters such as body length, rush speed for instantaneous swimming, water temperature, and presence/absence of nuptial coloration on fishway preference. T. hakonensis with nuptial coloration had greater body length and higher rush speeds than those without it. They also preferred the ice‐harbor fishway, whereas their shorter, uncolored counterparts preferred the stair and rock‐ramp alternatives. The environmental conditions selected by T. hakonensis changed according to their growth stage, as did fishway preference. Changes in fishway environmental conditions may have influenced the observed differences in fishway populations. It was thus confirmed that developing fishways with different flow velocities and water depths is effective in supporting the various life stages of T. hakonensis.