Natural flow regimes are critical for sustaining biodiversity and river integrity. Floods and droughts form an important component of river systems and control population sizes and species diversity across space and time. Modification of flow regimes, including disruption of the timing, magnitude and duration of flooding, is a global problem, and many new impoundments are planned for large river-floodplain ecosystems in the tropics. Flow modifications may cause dramatic non-linear responses in population sizes and have lasting effects through time, but such topics are poorly investigated over multi-year scales, especially in highly diverse tropical ecosystems. Using a long-term dataset from the Upper Paraná River floodplain, Brazil, I tested for threshold and legacy effects of fish assemblages to flood attributes, such as timing, magnitude, duration, rate of change and variation. Specifically, I hypothesized that long duration, high magnitude floods would elicit threshold responses in long-distance migratory fish species and these responses result in significant legacy effects detectable over multiple years. Consistent positive threshold responses to increasing flood duration and magnitude were detected for many species and not significantly correlated with reproductive guilds. Legacy effects were prevalent (i.e. identified for more than 90% of species) and including flood attributes from previous years increased variance explained in species abundances by 15-20% compared to contemporary flood attributes alone. Contrary to my hypotheses, flood duration did not elicit strong legacy effects and species from the same reproductive guild did not have similar legacy effects models. The prevalence of legacy effects across almost all species in this diverse study system highlights the need to consider such dynamics in other systems. My results provide targets for management and conservation actions, such as environmental flow releases from upstream reservoirs. Environmental flows releases may play a significant role in sustainability of the floodplain and other tropical floodplain ecosystems affected by impoundments.