Flow disturbance and introduced species can interact to influence population dynamics of riverine fish. Because climate change is predicted to promote larger, more frequent floods, understanding the interacting effects of extreme floods and introduced species is critical for the conservation of native fish. In New Zealand, native non-migratory galaxiid fishes face pressure from introduced trout through interspecific competition and predation. There is currently a lack of understanding around how galaxiid-trout relationships will change under future flow regimes. Following an extreme flood event in May 2021, we conducted a field survey which compared galaxiid population densities and individual growth along a gradient of flood magnitude to investigate how galaxiid populations have recovered from the major flood disturbance and the role of trout in mediating those dynamics. We found that galaxiid densities of +2 year size classes were least negatively affected by the flood event, compared to 1-2 year and young-of-the-year size classes. Compared to interspecific interactions shared with trout, intraspecific interactions had the greatest negative effect on native galaxiid growth. In summary, our results highlight that non-migratory galaxiid population dynamics result from a complex interplay between flood disturbance regimes and introduced trout densities, which presents a challenge for conservation of these species under climate change.