Although river floods and spates have a major influence on fish populations, few studies have examined the selective pressure on individuals and traits that favour their survival. In this study, the factors that potentially affect the survival of an amphidromous fish species, ayu Plecoglossus altivelis altivelis (Temminck & Schlegel), during a major spate were examined. Using otolith analyses, ayu in the Takahashi River, Okayama, Japan, were compared before (April; n = 50) and after (September; n = 32) a spate with regard to their respective hatch‐date distributions, standard body length and age at upstream migration, age at metamorphosis, and larval and juvenile growth rates. When comparing juvenile traits, surviving adult ayu grew faster than individuals collected before the spate. These findings suggest that juvenile growth rate is a key factor for enhancing subsequent survival and highlight the importance of conserving suitable nursery habitats to enhance fish survival during future floods.